Laboratoire Informatique d'Avignon

Simulated gastro-intestinal digestion is widely employed in many fields of food and nutritional sciences, as conducting human trials are often costly, resource intensive, and ethically disputable. As a consequence, in vitro alternatives that determine endpoints such as the bioaccessibility of nutrients and non-nutrients or the digestibility of macronutrients (e.g. lipids, proteins and carbohydrates) are used for screening and building new hypotheses. Various digestion models have been proposed, often impeding the possibility to compare results across research teams. For example, a large variety of enzymes from different sources such as of porcine, rabbit or human origin have been used, differing in their activity and characterization. Differences in pH, mineral type, ionic strength and digestion time, which alter enzyme activity and other phenomena, may also considerably alter results. Other parameters such as the presence of phospholipids, individual enzymes such as gastric lipase and digestive emulsifiers vs. their mixtures (e.g. pancreatin and bile salts), and the ratio of food bolus to digestive fluids, have also been discussed at length. In the present consensus paper, within the COST Infogest network, we propose a general standardised and practical static digestion method based on physiologically relevant conditions that can be applied for various endpoints, which may be amended to accommodate further specific requirements. A frameset of parameters including the oral, gastric and small intestinal digestion are outlined and their relevance discussed in relation to available in vivo data and enzymes. This consensus paper will give a detailed protocol and a line-by-line, guidance, recommendations and justifications but also limitation of the proposed model. This harmonised static, in vitro digestion method for food should aid the production of more comparable data in the future.

BACKGROUND: The Surviving Sepsis Campaign recommends targeting a mean arterial pressure of at least 65 mm Hg during initial resuscitation of patients with septic shock. However, whether this blood-pressure target is more or less effective than a higher target is unknown. METHODS: In a multicenter, open-label trial, we randomly assigned 776 patients with septic shock to undergo resuscitation with a mean arterial pressure target of either 80 to 85 mm Hg (high-target group) or 65 to 70 mm Hg (low-target group). The primary end point was mortality at day 28. RESULTS: At 28 days, there was no significant between-group difference in mortality, with deaths reported in 142 of 388 patients in the high-target group (36.6%) and 132 of 388 patients in the low-target group (34.0%) (hazard ratio in the high-target group, 1.07; 95% confidence interval [CI], 0.84 to 1.38; P=0.57). There was also no significant difference in mortality at 90 days, with 170 deaths (43.8%) and 164 deaths (42.3%), respectively (hazard ratio, 1.04; 95% CI, 0.83 to 1.30; P=0.74). The occurrence of serious adverse events did not differ significantly between the two groups (74 events [19.1%] and 69 events [17.8%], respectively; P=0.64). However, the incidence of newly diagnosed atrial fibrillation was higher in the high-target group than in the low-target group. Among patients with chronic hypertension, those in the high-target group required less renal-replacement therapy than did those in the low-target group, but such therapy was not associated with a difference in mortality. CONCLUSIONS: Targeting a mean arterial pressure of 80 to 85 mm Hg, as compared with 65 to 70 mm Hg, in patients with septic shock undergoing resuscitation did not result in significant differences in mortality at either 28 or 90 days. (Funded by the French Ministry of Health; SEPSISPAM ClinicalTrials.gov number, NCT01149278.).

Abstract In this article, we propose a solution procedure for the Elementary Shortest Path Problem with Resource Constraints (ESPPRC). A relaxed version of this problem in which the path does not have to be elementary has been the backbone of a number of solution procedures based on column generation for several important problems, such as vehicle routing and crew pairing. In many cases relaxing the restriction of an elementary path resulted in optimal solutions in a reasonable computation time. However, for a number of other problems, the elementary path restriction has too much impact on the solution to be relaxed or might even be necessary. We propose an exact solution procedure for the ESPPRC, which extends the classical label correcting algorithm originally developed for the relaxed (nonelementary) path version of this problem. We present computational experiments of this algorithm for our specific problem and embedded in a column generation scheme for the classical Vehicle Routing Problem with Time Windows. © 2004 Wiley Periodicals, Inc. NETWORKS, Vol. 44(3), 216–229 2004

Traveling salesman problems with profits (TSPs with profits) are a generalization of the traveling salesman problem (TSP), where it is not necessary to visit all vertices. A profit is associated with each vertex. The overall goal is the simultaneous optimization of the collected profit and the travel costs. These two optimization criteria appear either in the objective function or as a constraint. In this paper, a classification of TSPs with profits is proposed, and the existing literature is surveyed. Different classes of applications, modeling approaches, and exact or heuristic solution techniques are identified and compared. Conclusions emphasize the interest of this class of problems, with respect to applications as well as theoretical results.

A keyword query is the representation of the information need of a user, and is the result of a complex cognitive process which often results in under-specification. We propose an unsupervised method namely Latent Concept Modeling (LCM) for mining and modeling latent search concepts in order to recreate the conceptual view of the original information need. We use Latent Dirichlet Allocation (LDA) to exhibit highly-specific query-related topics from pseudo-relevant feedback documents. We define these topics as the latent concepts of the user query. We perform a thorough evaluation of our approach over two large ad-hoc TREC collections. Our findings reveal that the proposed method accurately models latent concepts, while being very effective in a query expansion retrieval setting.

SpeechBrain is an open-source and all-in-one speech toolkit. It is designed to facilitate the research and development of neural speech processing technologies by being simple, flexible, user-friendly, and well-documented. This paper describes the core architecture designed to support several tasks of common interest, allowing users to naturally conceive, compare and share novel speech processing pipelines. SpeechBrain achieves competitive or state-of-the-art performance in a wide range of speech benchmarks. It also provides training recipes, pretrained models, and inference scripts for popular speech datasets, as well as tutorials which allow anyone with basic Python proficiency to familiarize themselves with speech technologies.

These recommendations provide an evidence-based approach to the role of esophageal stents in the management of benign and malignant diseases. These guidelines have been developed under the auspices of the American College of Gastroenterology and its Practice Parameters Committee and approved by the Board of Trustees. The following guidelines are based on a critical review of the available scientific literature on the topic identified in Medline and PubMed (January 1992–December 2008) using search terms that included stents, self-expandable metal stents, self-expandable plastic stents, esophageal cancer, esophageal adenocarcinoma, esophageal squamous cell carcinoma, esophageal stricture, perforations, anastomotic leaks, tracheoesophageal fistula, and achalasia. These guidelines are intended for use by health-care providers and apply to adult, but not pediatric, patients. As with other practice guidelines, these guidelines are not intended to replace clinical judgment but rather to provide general guidelines applicable to the majority of patients. Clinicians need to integrate recommendations with their own clinical judgment, and with individual patient circumstances, values, and preferences. They are intended to be flexible, in contrast to standards of care, which are inflexible policies designed to be followed in every case. Specific recommendations are based on relevant published information. The quality of evidence and strength of recommendations have been assessed using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system, which is a system that has been adopted by multiple national and international societies. The GRADE system is based on a sequential assessment of quality of evidence, followed by assessment of the balance between benefits vs. downsides (harms, burden, and costs) and subsequent judgment regarding the strength of recommendation.

We investigate connectivity in the ad hoc network formed between vehicles that move on a typical highway. We use a common model in vehicular traffic theory in which a fixed point on the highway sees cars passing it that are separated by times with an exponentially distributed duration. We obtain the distribution of the distances between the cars, which allows us to use techniques from queuing theory to study connectivity. We obtain the Laplace transform of the probability distribution of the connectivity distance, explicit expressions for the expected connectivity distance, and the probability distribution and expectation of the number of cars in a platoon. Then, we conduct extensive simulation studies to evaluate the obtained results. The analytical model that we present is able to describe the effects of various system parameters, including road traffic parameters (i.e., speed distribution and traffic flow) and the transmission range of vehicles, on the connectivity. To more precisely study the effect of speed on connectivity, we provide bounds obtained using stochastic ordering techniques. Our approach is based on the work of Miorandi and Altman, which transformed the problem of connectivity distance distribution into that of the distribution of the busy period of an equivalent infinite server queue. We use our analytical results, along with common road traffic statistical data, to understand connectivity in vehicular ad hoc networks.

ABSTRACT Objective To generate guidance for detailed uterine niche evaluation by ultrasonography in the non‐pregnant woman, using a modified Delphi procedure amongst European experts. Methods Twenty gynecological experts were approached through their membership of the European Niche Taskforce. All experts were physicians with extensive experience in niche evaluation in clinical practice and/or authors of niche publications. By means of a modified Delphi procedure, relevant items for niche measurement were determined based on the results of a literature search and recommendations of a focus group of six Dutch experts. It was predetermined that at least three Delphi rounds would be performed (two online questionnaires completed by the expert panel and one group meeting). For it to be declared that consensus had been reached, a consensus rate for each item of at least 70% was predefined. Results Fifteen experts participated in the Delphi procedure. Consensus was reached for all 42 items on niche evaluation, including definitions, relevance, method of measurement and tips for visualization of the niche. A niche was defined as an indentation at the site of a Cesarean section with a depth of at least 2 mm. Basic measurements, including niche length and depth, residual and adjacent myometrial thickness in the sagittal plane, and niche width in the transverse plane, were considered to be essential. If present, branches should be reported and additional measurements should be made. The use of gel or saline contrast sonography was preferred over standard transvaginal sonography but was not considered mandatory if intrauterine fluid was present. Variation in pressure generated by the transvaginal probe can facilitate imaging, and Doppler imaging can be used to differentiate between a niche and other uterine abnormalities, but neither was considered mandatory. Conclusion Consensus between niche experts was achieved regarding ultrasonographic niche evaluation. © 2018 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.

Coupling the high data rates of IEEE 802.11p-based VANETs and the wide coverage area of 3GPP networks (e.g., UMTS), this paper envisions a VANET-UMTS integrated network architecture. In this architecture, vehicles are dynamically clustered according to different related metrics. From these clusters, a minimum number of vehicles, equipped with IEEE 802.11p and UTRAN interfaces, are selected as vehicular gateways to link VANET to UMTS. Issues pertaining to gateway selection, gateway advertisement and discovery, service migration between gateways (i.e., when serving gateways lose their optimality) are all addressed and an adaptive mobile gateway management mechanism is proposed. Simulations are carried out using NS2 to evaluate the performance of the envisioned architecture incorporating the proposed mechanisms. Encouraging results are obtained in terms of high data packet delivery ratios and throughput, reduced control packet overhead, and minimized delay and packet drop rates.

The intelligent transportation systems ITS cause a significant passion since the appearance of new inter-vehicles communication mechanisms based on mobile networks. The wireless ad hoc networks, completely distributed and not depending on infrastructures, allow the fast and cheap development of such mechanisms. This article concerns multicast in wireless ad-hoc networks applied to ITS. We propose a new protocol called IVG inter-vehicles geocast which consists in informing all the vehicles of a highway about any danger such as an accident or any other obstacle. In this case, risk areas are determined according to the driving direction and the positioning of the vehicles. These vehicles define a restricted broadcast group, so-called, multicast group. Multicast group, contrary to the classical methods, which use node identities, is defined temporally and dynamically by the location, speed and driving direction of vehicles. Some simulations thanks to Glomosim tool, for which we have defined a model for the road transport, and studies of the complexity are given. The results show that IVG is an efficient broadcast method for secure highway transportation and reduces the number of useful messages.

We consider a noncooperative interaction among a large population of mobiles that interfere with each other through many local interactions. The first objective of this paper is to extend the evolutionary game framework to allow an arbitrary number of mobiles that are involved in a local interaction. We allow for interactions between mobiles that are not necessarily reciprocal. We study 1) multiple-access control in a slotted Aloha-based wireless network and 2) power control in wideband code-division multiple-access wireless networks. We define and characterize the equilibrium (called evolutionarily stable strategy) for these games and study the influence of wireless channels and pricing on the evolution of dynamics and the equilibrium.

Large Language Models (LLMs) have demonstrated remarkable versatility in recent years, offering potential applications across specialized domains such as healthcare and medicine.Despite the availability of various open-source LLMs tailored for health contexts, adapting general-purpose LLMs to the medical domain presents significant challenges.In this paper, we introduce BioMistral, an open-source LLM tailored for the biomedical domain, utilizing Mistral as its foundation model and further pre-trained on PubMed Central.We conduct a comprehensive evaluation of BioMistral on a benchmark comprising 10 established medical question-answering (QA) tasks in English.We also explore lightweight models obtained through quantization and model merging approaches.Our results demonstrate BioMistral's superior performance compared to existing open-source medical models and its competitive edge against proprietary counterparts.Finally, to address the limited availability of data beyond English and to assess the multilingual generalization of medical LLMs, we automatically translated and evaluated this benchmark into 7 other languages.This marks the first large-scale multilingual evaluation of LLMs in the medical domain.Datasets, multilingual evaluation benchmarks, scripts, and all the models obtained during our experiments are freely released.

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

RATIONALE: Ventilator-associated pneumonia (VAP) causes substantial morbidity and mortality. The influence of subglottic secretion drainage (SSD) in preventing VAP remains controversial. OBJECTIVES: To determine whether SSD reduces the overall incidence of microbiologically confirmed VAP. METHODS: Randomized controlled clinical trial conducted at four French centers. A total of 333 adult patients intubated with a tracheal tube allowing drainage of subglottic secretions and expected to require mechanical ventilation for ≥48 hours was included. Patients were randomly assigned to undergo intermittent SSD (n = 169) or not (n = 164). MEASUREMENTS AND MAIN RESULTS: Primary outcome was the overall incidence of VAP based on quantitative culture of distal pulmonary samplings performed after each clinical suspicion. Other outcomes included incidence of early- and late-onset VAP, duration of mechanical ventilation, and hospital mortality. Microbiologically confirmed VAP occurred in 67 patients, 25 of 169 (14.8%) in the SSD group and 42 of 164 (25.6%) in the control group (P = 0.02), yielding a relative risk reduction of 42.2% (95% confidential interval, 10.4-63.1%). Using the Day 5 threshold, the beneficial effect of SSD in reducing VAP was observed in both early-onset VAP (2 of 169 [1.2%] patients undergoing SSD vs. 10 of 164 [6.1%] control patients; P = 0.02) and late-onset VAP (23 of 126 [18.6%] patients undergoing SSD vs. 32 of 97 [33.0%] control patients; P = 0.01). VAP was clinically suspected at least once in 51 of 169 (30.2%) patients undergoing SSD and 60 of 164 (36.6%) control patients (P = 0.25). No significant between-group differences were observed in duration of mechanical ventilation and hospital mortality. CONCLUSIONS: Subglottic secretion drainage during mechanical ventilation results in a significant reduction in VAP, including late-onset VAP. Clinical trial registered with www.clinicaltrials.gov (NCT00219661).

Collaboration et al., (2021). The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained. Journal of Open Source Software, 6(58), 2807, https://doi.org/10.21105/joss.02807

OBJECTIVE: To disentangle the impact of adherence from that of injecting drug status and depressive syndrome on HIV clinical progression in a cohort of highly active antiretroviral therapy (HAART)-treated HIV patients infected through drug use. DESIGN: MANIF 2000 is a French cohort of HIV-infected drug users with scheduled medical visits every 6 months. Only patients enrolled in the MANIF 2000 cohort who had a CD4 cell count >200 cells/microl at HAART initiation were selected. The follow-up period included all post-HAART initiation visits. METHODS: HIV clinical progression was defined as either AIDS-related death or reaching a CD4 level <200 cells/microl. Adherence was assessed using a self-administered questionnaire and a structured face-to-face interview. Depressive symptoms were evaluated by a Center for Epidemiologic Studies Depression Scale (CES-D) score at each visit. Cox proportional hazards model was used to calculate crude and adjusted relative hazards and 95% confidence intervals and thus identify independent predictors of clinical progression. RESULTS: Of the 305 HAART-treated patients in the cohort, 243 had CD4 cell count >200 cells/microl at HAART initiation. At the first visit after HAART initiation, median CD4 cell count was 466 cells/microl and 45% had undetectable viral load. Injecting drug users accounted for 17% of the study group. Over the follow-up period, 32 patients experienced HIV clinical progression. Probable depression was encountered in 46% of patients and non-adherence in 31% of the sample. After adjustment on baseline CD4 cell count, predictors of clinical progression were: having a higher level of cumulative non-adherence over the follow-up period [HR (95% CI)=1.2 (1.1-1.3) per 10% increase] and having a high score of depressive symptoms following HAART initiation [HR (95% CI)=5.3 (2.21-3.0)]. CONCLUSIONS: Although depressive syndrome is known to influence non-adherence behaviours that are amongst the major reasons for clinical progression, it is also a predictor of clinical progression in HIV-infected intravenous drug users on HAART, independently of non-adherence behaviours. HIV care providers should be more sensitive to depressive symptoms in order to detect them early and supply HIV patients with specific care. Further research is needed to determine whether treating depressive symptoms may improve adherence and thus delay disease progression and mortality.

OBJECTIVE: To determine the clinical outcome of children with chronic recurrent multifocal osteomyelitis (CRMO). METHODS: We retrospectively reviewed clinical, biological and radiological data of children with CRMO at five French paediatric centres. Outcome data were obtained through review of hospital charts and questionnaires sent to all patients to assess disease activity and educational and vocational achievement. RESULTS: Forty patients were assessed (34 females and 6 males) with a median age at diagnosis of 11.5 yrs (range 2-17). Median number of initial bony lesions was 2 at onset, and 3.5 over disease course. Median time since diagnosis was 3.5 yrs (range 0.5-15) and median duration of active disease 2.7 yrs (range 0.5-13.5). Nine (22.5%) patients had psychological or physical sequelae. Twenty-nine children (72.5%) responded to the questionnaire. Twenty-six had no physical disability as judged by the HAQ 0-1, two had moderate disability (HAQ: 1-2) and one had severe disability (HAQ: 2-3). Seventeen patients (58.6%) had active disease at follow-up (after 6 months to 15 yrs since diagnosis) and continued to have pain (median value of visual analogue scale: 10/100). CRMO had interfered with patient's education in two cases. CONCLUSIONS: Clinical outcome of children with CRMO is generally good, but a sizeable proportion of patients have active disease at follow-up, and a minority of patients can have a severe and prolonged disease course despite intensive treatments. Further studies are required to determine predictive factors for severe disease.

BACKGROUND AND STUDY AIMS: Endoscopic submucosal dissection (ESD) is a technique for "en bloc" resection of superficial tumors of the gastrointestinal tract. In France, experience with this technique is still limited. We wanted to assess the development of ESD in France, with special attention to short term outcomes. PATIENTS AND METHODS: Members of the Société Française d'Endoscopie Digestive (SFED) who declared performing ESD reported their cases prospectively on a voluntary basis. Demographic, clinical, and technical data, and the results of immediate complications were collected. Case reports were completed prospectively by each investigator before pooled analysis. RESULTS: A total of 188 consecutive case reports were collected from 16 centers. The median case mix per center was 6 patients (range 1-43). The lesion sites treated by ESD were the stomach (n = 75), esophagus (n = 27), duodenum (n = 1), cecum (n = 2), right colon (n = 3), transverse colon (n = 5), sigmoid (n = 3), and rectum (n = 72). The median size of the lesions was 26 mm (range 2-150 mm). En bloc resection was achieved in 77.1% of cases, with complete R0 resection in 72.9%. Histopathology results showed high grade dysplasia or superficial cancer in 71.2%. The median duration of ESD was 105 minutes (range 20-450 minutes). The short term morbidity was 29.2% including 34 cases of perforation (18.1%), and 21 hemorrhages (11.2%) during the 24 hours following ESD, 89% of which were managed conservatively or endoscopically. CONCLUSION: In this early experience, the feasibility of ESD appeared to be good but R0 resection and complication rates did not match those reported by Japanese authors and must be improved by an extended practice.

Looking at the different points highlighted in this article, we affirm that forensic applications of speaker recognition should still be taken under a necessary need for caution. Disseminating this message remains one of the most important responsibilities of speaker recognition researchers.