Miracle-dz/UniFAR-FTUs huggingface dataset:
Static/Dynamic Analyses for Validation and Improvements of Multi-Model HPC Applications. (Analyse statique/dynamique pour la validation et l'amélioration des applications parallèles multi-modèles)

Supercomputing plays an important role in several innovative fields, speeding up prototyping or validating scientific theories. However, supercomputers are evolving rapidly with now millions of processing units, posing the questions of their programmability. Despite the emergence of more widespread and functional parallel programming models, developing correct and effective parallel applications still remains a complex task. Although debugging solutions have emerged to address this issue, they often come with restrictions. However programming model evolutions stress the requirement for a convenient validation tool able to handle hybrid applications. Indeed as current scientific applications mainly rely on the Message Passing Interface (MPI) parallel programming model, new hardwares designed for Exascale with higher node-level parallelism clearly advocate for an MPI+X solutions with X a thread-based model such as OpenMP. But integrating two different programming models inside the same application can be error-prone leading to complex bugs - mostly detected unfortunately at runtime. In an MPI+X program not only the correctness of MPI should be ensured but also its interactions with the multi-threaded model, for example identical MPI collective operations cannot be performed by multiple nonsynchronized threads. This thesis aims at developing a combination of static and dynamic analysis to enable an early verification of hybrid HPC applications. The first pass statically verifies the thread level required by an MPI+OpenMP application and outlines execution paths leading to potential deadlocks. Thanks to this analysis, the code is selectively instrumented, displaying an error and synchronously interrupting all processes if the actual scheduling leads to a deadlock situation.
Biological, Psychological, and Social Predictors of Longevity Among Utah Centenarians

Studies of longevity among centenarians examine biological, psychological, and social factors, yet few consider these components concurrently. This study explores such factors individually and collectively, as they are related to days lived past the age of 100 years. Data from 268 family members of centenarians identified in the State of Utah between 2008 and 2015 were used in negative binomial models predicting number of days lived among the centenarians. Findings suggested that sleep latency (biological), life satisfaction (psychological), and attachment closeness (social) were predictive factors of more days lived within individual models. When considered together, sleep latency and life satisfaction remained significant predictors of days lived. Although biological factors are commonly considered in relation to longevity, this study further indicates that psychological and social factors may play important roles in life expectancy. Further examination is needed to explore how these factors link additionally to active life expectancy.
Posterior Sloping Angle of the Capital Femoral Physis: Interobserver and Intraobserver Reliability Testing and Predictor of Bilaterality

The management of the contralateral hip after unilateral slipped capital femoral epiphysis (SCFE) is controversial. The aims of this study were to assess the interobserver and intraobserver reliability of the posterior sloping angle (PSA) as described by Barrios et al (J Pediatr Orthop. 2005;25:445-449) and whether it can be used as a predictor of need for prophylactic pinning of the contralateral hip. The PSA was measured by 4 different surgeons on 2 separated occasions in 47 unaffected contralateral hips after unilateral SCFE. The interobserver intraclass correlation coefficient (ICC) was 0.83 (excellent) for the first set of measurements and 0.74 (fair to good) for the second set of measurements. Measurement of the intraobserver ICC revealed an excellent agreement (ICC > 0.75) in 3 of the 4 surgeons and fair to good agreement in 1 of the surgeons (ICC between 0.4 and 0.74). Comparison of the PSA measurements of the first author (M.Z.) with a control group of 20 hips revealed that the PSA was significantly higher (P < 0.05) in the group of patients that eventually had a contralateral slip when compared with the PSA of patients in the study group who did not slip and with normal hips in the control group. Patients with contralateral SCFE that did not slip had a significantly higher PSA (P < 0.05) when compared with normal individuals. A PSA of 14.5 degrees or more is recommended for prophylactic pinning of the contralateral hip. The number needed to treat (NNT) at this cut off to avoid 1 future slip was calculated to be 1.9.
Efficient and Smooth RRT Motion Planning Using a Novel Extend Function for Wheeled Mobile Robots

In this paper we introduce a novel RRT extend function for wheeled mobile robots. The approach computes closed-loop forward simulations based on the kinematic model of the robot and enables the planner to efficiently generate smooth and feasible paths that connect any pairs of states. We extend the control law of an existing discontinuous state feedback controller to make it usable as an RRT extend function and prove that all relevant stability properties are retained. We study the properties of the new approach as extender for RRT and RRT* and compare it systematically to a spline-based approach and a large and small set of motion primitives. The results show that our approach generally produces smoother paths to the goal in less time with smaller trees. For RRT*, the approach produces also the shortest paths and achieves the lowest cost solutions when given more planning time.
Integrating ear and scalp acupuncture techniques into the care of blast-injured United States military service members with limb loss.

Princeof Chungshan. However, within the U.S. Armed Forces, theincorporation of acupuncture into modern military medicalpractice is a relatively new development.The effectiveness of acupuncture is well known to manycultures. Its widespread use is primarily credited to the Chi-nese and to Mao Zedong’s legion of “barefoot doctors” (indegenous practitioners) who promulgated the use ofacupuncture during the period of the Chinese Cultural Rev-olution (1949–1970s). Although acupuncture continues togain popularity in civilian sectors across the globe, use ofacupuncture techniques by U.S. military medical personnelis still a relatively nascent process. Given the unique natureof blast and combat-related injuries sustained by Americanmilitary service members during current operations inAfghanistan and Iraq, ear and scalp acupuncture techniqueshave promise in helping to reduce the pain associated withbattlefield wounds.One of the first persons to introduce acupuncture to U.S.military medical personnel was the (then) Army Major (Dr.)Norman Rich, who, along with Army Lieutenant Colonel(Dr.) Francis Dimond, Jr., reported on their experiences atthe 2nd Surgical Hospital in Vietnam, in a 1967 edition of
AN INTRODUCTION TO SOCIAL CONSTRUCTIONISM

The social constructionism perspective says that we never know what universal true or false is, what is good or bad, right or wrong; we know only stories about true, false, good, bad, right or wrong. The social constructionism abandons the idea of constructivist that individual’s mind represents a mirror of reality. The constructionism is focused on relations and sustains the individual’s role in social construction of realities. „Maps for the same territory” seems to be the essence of constructivist. The social constructionism is not interested to create maps; it surprises the processes that maps form. Our maps are formed from our experience and how we perceive them. All our maps are differing maps of the same world. Each of us creates our own worlds from our perceptions of the actual world. The social constructionism sees the language, the communication and the speech as having the central role of the interactive process through which we understand the world and ourselves.
In vitro drug testing in patients with acute leukemia with incubations mimicking in vivo intracellular drug concentrations

The differential staining cytotoxicity (DiSC) assay was evaluated as a predictive test for response to therapy in patients with acute non‐lymphoblastic leukemia. Incubations were designed in such a way that the intracellular concentrations of cytostatic drugs in vitro parallelled those in vivo. Leukemic cells were isolated from 53 patients with acute non‐lymphocytic leukemia. 13 of these patients died early due to supportive care failure and were not evaluable for the predictive drug testing. Of the remaining 40 patients, 25 entered a complete remission (CR) and 15 had a resistant disease (RD). According to the patients randomization to therapy the cells were incubated with anthracyclines and Ara‐C separately and in combination. After 4 days of culturing in liquid medium the in vitro cytotoxicity was determined by dye exclusion according to Weisenthal. The cytotoxic effect in vitro was significantly higher on cells from patients who achieved a CR compared to patients with RD after incubations with anthracyclines 0.2 μmol/l (p ≤ 0.005), Ara‐C 0.5 μmol/l (p ≤ 0.05) and with the combination of anthracyclines with Ara‐C (p ≤ 0.0005). The best predictive value was achieved when incubations with 0.2 μmol/l anthracyclines and 0.5 μmol/l Ara‐C were analyzed together. With these incubations cells from 20 out of 21 patients who achieved CR showed either ≤ 60% surviving cells after the anthracycline incubation or ≤ 35% surviving cells after the Ara‐C incubation. Cells from 11 out of 13 patients with RD did not fulfill either of these criteria. In vitro drug sensitivity was signiñcantly correlated to a prolonged survival (p < 0.01). We conclude that, when performed with incubations that mimic in vivo tumor cell exposure to cytostatic drugs, the DiSC assay shows a high correlation to clinical outcome for patients with acute non‐lymphocytic leukemia.
The state of regional therapy in the management of metastatic colorectal cancer to the liver

ABSTRACT Colorectal cancer (CRC) is one of the leading causes of cancer-related mortality in the United States. Most colorectal cancer patients die from advanced disease, and two-thirds of CRC deaths are due to liver metastases. Liver resection provides the best curative option for patients with colorectal liver metastases (CRLM), yet only 20% of those patients are eligible for liver metastases resection for curative intent. Loco-regional treatment of CRLM may provide additional benefits in terms of down-staging for resection and prolonged hepatic disease control. This review focusses on hepatic arterial infusion, radioembolization and chemoembolization.
TAZ Promotes PC2 Degradation through a SCFβ-Trcp E3 Ligase Complex

ABSTRACT Studies of a TAZ knockout mouse reveal a novel function of the transcriptional regulator TAZ, that is, as a binding partner of the F-box protein β-Trcp. TAZ−/− mice develop polycystic kidney disease (PKD) and emphysema. The calcium-permeable cation channel protein polycystin 2 (PC2) is overexpressed in kidneys of TAZ−/− mice as a result of decreased degradation via an SCFβ-Trcp E3 ubiquitin ligase pathway. Replacements of serines in a phosphodegron motif in TAZ prevent β-Trcp binding and PC2 degradation. Coexpression of a cytoplasmic fragment of polycystin 1 blocks the PC2-TAZ interaction and prevents TAZ-mediated degradation of PC2. Depletion of TAZ in zebrafish also results in a cystic kidney accompanied by overexpression of PC2. These results establish a common role of TAZ across vertebrate species in a protein degradation pathway regulated by phosphorylation and implicate deficiencies in this pathway in the development of PKD.
Characterizing user mobility using mobile sensing systems

Recent technological advances and the ever-greater developments in sensing and computing continue to provide new ways of understanding our daily mobility. Smart devices such as smartphones or smartwatches can, for instance, provide an enhanced user experience based on different sets of built-in sensors that follow every user action and identify its environment. Monitoring solutions such as these, which are becoming more and more common, allows us to assess human behavior and movement at different levels. In this article, extended from previous work, we focus on the concept of human mobility and explore how we can exploit a dataset collected opportunistically from multiple participants. In particular, we study how the different sensor groups present in most commercial smart devices can be used to deliver mobility information and patterns. In addition to traditional motion sensors that are obviously important in this field, we are also exploring data from physiological and environmental sensors, including new ways of displaying, understanding, and analyzing data. Furthermore, we detail the need to use methods that respect the privacy of users and investigate the possibilities offered by network traces, including Wi-Fi and Bluetooth communication technologies. We finally offer a mobility assistant that can represent different user characteristics anonymously, based on a combination of Wi-Fi, activity data, and graph theory.
Cdc 6 protein causes premature entry into S phase in a mammalian cell-free system

We exploit an improved mammalian cell-free DNA replication system to analyse quiescence and Cdc6 function. Quiescent 3T3 nuclei cannot initiate replication in S phase cytosol from HeLa or 3T3 cells. Following release from quiescence, nuclei become competent to initiate semiconservative DNA replication in S phase cytosol, but not in G0 phase cytosol. Immunoblots show that quiescent cells lack Cdc6 and that minichromosome maintenance (MCM) proteins are not associated with chromatin. Competence of G1 phase nuclei to replicate in vitro coincides with maximum Cdc6 accumulation and MCM protein binding to chromatin in vivo. Addition of recombinant Cdc6 to permeabilized, but not intact, G1 nuclei causes up to 82% of the nuclei to initiate and accelerates G1 progression, making nuclei competent to replicate prematurely.
MAPPING FOR SPEAKER DIARIZATION IN NOISY CONDITIONS

Speaker diarization in noisy conditions is addressed in this paper. The regression-based DNN is first adopted to map the noisy acoustic features to the clean features, and then consensus clustering of the original and mapped features is used to fuse the diarization results. The experiments are conducted on the IFLY-DIAR-II database, which is a Chinese talk show database with various noise types, such as music, applause and laughter. Compared to the baseline system using PLP features, a 21.26% relative DER improvement can be achieved using the proposed algorithm. Index Terms Speaker diarization, deep neural networks, feature mapping, consensus clustering
The Arabidopsis DESPERADO/AtWBC11 Transporter Is Required for Cutin and Wax Secretion1[C][W]

The cuticle fulfills multiple roles in the plant life cycle, including protection from environmental stresses and the regulation of organ fusion. It is largely composed of cutin, which consists of C16-18 fatty acids. While cutin composition and biosynthesis have been studied, the export of cutin monomers out of the epidermis has remained elusive. Here, we show that DESPERADO (AtWBC11) (abbreviated DSO), encoding a plasma membrane-localized ATP-binding cassette transporter, is required for cutin transport to the extracellular matrix. The dso mutant exhibits an array of surface defects suggesting an abnormally functioning cuticle. This was accompanied by dramatic alterations in the levels of cutin monomers. Moreover, electron microscopy revealed unusual lipidic cytoplasmatic inclusions in epidermal cells, disappearance of the cuticle in postgenital fusion areas, and altered morphology of trichomes and pavement cells. We also found that DSO is induced by salt, abscisic acid, and wounding stresses and its loss of function results in plants that are highly susceptible to salt and display reduced root branching. Thus, DSO is not only essential for developmental plasticity but also plays a vital role in stress responses.
Parenteral Adjuvant Activities of Escherichia coli Heat-Labile Toxin and Its B Subunit for Immunization of Mice against Gastric Helicobacter pyloriInfection

ABSTRACT The heat-labile toxin (LT) of Escherichia coli is a potent mucosal adjuvant that has been used to induce protective immunity against Helicobacter felis and Helicobacter pylori infection in mice. We studied whether recombinant LT or its B subunit (LTB) has adjuvant activity in mice when delivered withH. pylori urease antigen via the parenteral route. Mice were immunized subcutaneously or intradermally with urease plus LT, recombinant LTB, or a combination of LT and LTB prior to intragastric challenge with H. pylori. Control mice were immunized orally with urease plus LT, a regimen shown previously to protect against H. pylori gastric infection. Parenteral immunization using either LT or LTB as adjuvant protected mice againstH. pylori challenge as effectively as oral immunization and enhanced urease-specific immunoglobulin G (IgG) responses in serum as effectively as aluminum hydroxide adjuvant. LT and LTB had adjuvant activity at subtoxic doses and induced more consistent antibody responses than those observed with oral immunization. A mixture of a low dose of LT and a high dose of LTB stimulated the highest levels of protection and specific IgG in serum. Urease-specific IgG1 and IgG2a antibody subclass responses were stimulated by all immunization regimens tested, but relative levels were dependent on the adjuvant used. Compared to parenteral immunization with urease alone, LT preferentially enhanced IgG1, while LTB or the LT-LTB mixture preferentially enhanced IgG2a. Parenteral immunization using LT or LTB as adjuvant also induced IgA to urease in the saliva of some mice. These results show that LT and LTB stimulate qualitatively different humoral immune responses to urease but are both effective parenteral adjuvants for immunization of mice against H. pyloriinfection.
Development of thermodynamic models for simulating probe dissociation profiles in fluorescence in situ hybridization

Stringency in ribosomal RNA (rRNA)‐targeted fluorescence in situ hybridization (FISH) is typically adjusted with formamide, and the optimum formamide concentration at which the probe can hybridize with the target rRNA, but not with rRNAs with mismatches, is to be found experimentally. This is a difficult task when target or closest non‐target organisms are not available in pure culture, or when there are numerous non‐targets of concern. The objective of this work was to formulate mechanistic models capable of simulating the effect of formamide on probe dissociation. Using a previously described equilibrium model of FISH [Yilmaz and Noguera (2004) Applied and Environmental Microbiology 70(12):7126‐7139] as the basis, the effect of formamide on free energy changes of probe–target duplex formation (ΔG 10 ) and folding of target region (ΔG 30 ) was simulated to be linear, and models differing in the definitions of the slopes of these relationships (m1 and m3) were calibrated using experimental dissociation profiles for 27 probes targeting the 16S rRNA of Escherichia coli (E. coli). A good level of predictive power was obtained when m1 was linearly related to probe length and when m3 was made proportional to ΔG 30 . The effect of single mismatches on probe dissociation with formamide was also studied, although at a preliminary level. The expected changes in ΔG 10 with the introduction of mismatches were not sufficient to capture the overall trends of mismatched dissociation profiles. In conclusion, this study offers the first theoretical method to calculate dissociation profiles for perfectly matched probes, and suggests a direction to systematically evaluate the effect of formamide on mismatched probes. Biotechnol. Bioeng. 2007;96: 349–363. © 2006 Wiley Periodicals, Inc.
Risk of Extended Viral Resistance in Human Immunodeficiency Virus-1-Infected Mozambican Children After First-Line Treatment Failure

Background: Resistant virus may be selected by sub-optimal control of HIV-1 replication during antiretroviral treatment. The incidence and profile of resistance in children receiving World Health Organization-recommended treatment remains to be evaluated on a large scale. Goals: Assessment of the frequency and profile of resistant virus in HIV-1-infected children, treated for at least 6 months with stavudine/zidovudine + lamivudine + nevirapine and presenting virological failure in a large access program in Maputo, Mozambique. Results: Cross-sectional evaluation of plasma HIV-1 viral load (VL) in 495 evaluable children among 512 treated for at least 6 months showed that 360 (72.7%) had a VL of <50 copies/mL of HIV-1 RNA. Genotypic resistance tests were performed in the 84 available samples from the 135 treated children with VL ≥50 copies/mL: 92% of the viruses were resistant to lamivudine and/or nevirapine, and 15% were resistant to stavudine. Twenty children (24%) harbored virus with a extended spectrum of cross-resistance defined as resistance to the 3 drugs of the combination received by the child and/or at least 1 resistance to a drug to which the child had never been exposed (abacavir: 5%, tenofovir: 6%, didanosine: 3.5% and the new generation non nucleoside inhibitor, etravirine: 6%). The only factor identified by multivariate analysis as being associated with this extended resistance profile was the duration of treatment (aOR: 6.67 [95% CI: 1.24–35.93], P = 0.015 for treatment >24 months) with a per month increase of 1.09 (1.02–1.16) P = 0.007. Conclusions: Residual viral replication in children receiving stavudine/zidovudine + lamivudine + nevirapine treatment is associated with a time-dependent risk of acquiring cross-resistance, including resistance to drugs currently used for second-line treatment and also to the new generation of non nucleoside reverse transcritpase inhibitors.
Predictive and Anticipatory Computing

Encyclopedia of Copyright © 201 Abstract Predictive computation is the path that leads from reaction-based forms of computing to anticipatory forms of computing. It reflects the long-term goal of understanding and emulating the performance of the living. Prediction is informed by the past; probability underscores the gamut of predictive types. Anticipation implies awareness of past, present, and future. It underlies evolution and thus holds promise for realizing artificial adaptive systems. The possibility space is where anticipation is substantiated. Improved understanding of biological processes, paralleled by vastly scaled-up and diversified computer performance, has triggered a variety of engineering successes (mobile computing, robotics, artificial intelligence, the Internet-of-Everything, etc.). These have made predictive and anticipatory computing part of the new ecology of computation.