Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated Metagenomic and Metatranscriptomic Analyses of Microbial Communities in the Meso- and Bathypelagic Realm of North Pacific Ocean

Although emerging evidence indicates that deep-sea water contains an untapped reservoir of high metabolic and genetic diversity, this realm has not been studied well compared with surface sea water. The study provided the first integrated meta-genomic and -transcriptomic analysis of the microbial communities in deep-sea water of North Pacific Ocean. DNA/RNA amplifications and simultaneous metagenomic and metatranscriptomic analyses were employed to discover information concerning deep-sea microbial communities from four different deep-sea sites ranging from the mesopelagic to pelagic ocean. Within the prokaryotic community, bacteria is absolutely dominant (~90%) over archaea in both metagenomic and metatranscriptomic data pools. The emergence of archaeal phyla Crenarchaeota, Euryarchaeota, Thaumarchaeota, bacterial phyla Actinobacteria, Firmicutes, sub-phyla Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria, and the decrease of bacterial phyla Bacteroidetes and Alphaproteobacteria are the main composition changes of prokaryotic communities in the deep-sea water, when compared with the reference Global Ocean Sampling Expedition (GOS) surface water. Photosynthetic Cyanobacteria exist in all four metagenomic libraries and two metatranscriptomic libraries. In Eukaryota community, decreased abundance of fungi and algae in deep sea was observed. RNA/DNA ratio was employed as an index to show metabolic activity strength of microbes in deep sea. Functional analysis indicated that deep-sea microbes are leading a defensive lifestyle.
Machine-Learning-Guided Selectively Unsound Static Analysis

We present a machine-learning-based technique for selectively applying unsoundness in static analysis. Existing bug-finding static analyzers are unsound in order to be precise and scalable in practice. However, they are uniformly unsound and hence at the risk of missing a large amount of real bugs. By being sound, we can improve the detectability of the analyzer but it often suffers from a large number of false alarms. Our approach aims to strike a balance between these two approaches by selectively allowing unsoundness only when it is likely to reduce false alarms, while retaining true alarms. We use an anomaly-detection technique to learn such harmless unsoundness. We implemented our technique in two static analyzers for full C. One is for a taint analysis for detecting format-string vulnerabilities, and the other is for an interval analysis for buffer-overflow detection. The experimental results show that our approach significantly improves the recall of the original unsound analysis without sacrificing the precision.
Mismatch Effect on CT Specimen Mechanical Effect and Consequences on the Weld Toughness Characterization

The welded joints are particularly sensitive areas in the structures in terms of harmfulness of defects. Given the complexity of the problem (geometry poorly controlled, multi-material aspect, the potential influence of residual stresses), the tests are conducted based on pessimistic assumptions that can wrap all the uncertainties of the problem. In the case of a defect assessment, the considered toughness is deduced from conventional characterization tests with a crack in the welding, considering the current standards, ISO 12135 [1] or ASTM E-1820 [ 2] which are valid only for an homogeneous specimen. In 2010, a new standard ISO 16563 [3] was published to address the specificity of welded joints. If it covers some of the difficulties, it remains incomplete. In nuclear piping, welds have a mismatch M, ie the ratio between the yield strength of the weld metal and the base metal, usually greater than 1: this avoids any problem of strain localization at the junction and ensure that the stresses in the base metal are also easily supported by the welded joint. In this configuration, it turns out that for a given mechanical loading, a crack in the weld located generally has a solicitation, quantified by the parameter J, less (depending on the size of the junction) to those that would see the same crack located in the base metal. Unfortunately, this phenomenon exists also potentially for a characterization test, which would overestimate the true toughness of the welded joint. Plasticity that develops from the crack tip can quickly reach this interface and be affected. To evaluate this phenomenon, we considered two types of representative welded joint (PWR secondary loop ferritic weld and a 316 stainless steel weld) and performed a F.E. analysis of the multi-material CT specimen mechanical answer and on the η coefficient conventionally used to derive the plastic component of J from the area under the curve force-opening displacement.Copyright © 2011 by ASME
Beclin 1 Is Required for Starvation-Enhanced, but Not Rapamycin-Enhanced, LC3-Associated Phagocytosis of Burkholderia pseudomallei in RAW 264.7 Cells

ABSTRACT LC3-associated phagocytosis (LAP) of Burkholderia pseudomallei by murine macrophage (RAW 264.7) cells is an intracellular innate defense mechanism. Beclin 1, a protein with several roles in autophagic processes, is known to be recruited to phagosomal membranes as a very early event in LAP. We sought to determine whether knockdown of Beclin 1 by small interfering RNA (siRNA) would affect recruitment of LC3 and subsequent LAP of infecting B. pseudomallei. Both starvation and rapamycin treatment can induce Beclin 1-dependent autophagy. Therefore, we analyzed the consequences of Beclin 1 knockdown for LAP in infected cells that had been either starved or treated with rapamycin by determining the levels of bacterial colocalization with LC3 and intracellular survival. Concurrently, we confirmed the location of bacteria as either contained in phagosomes or free in the cytoplasm. We found that both rapamycin and starvation treatment enhanced LAP of B. pseudomallei but that the rapamycin response is Beclin 1 independent whereas the starvation response is Beclin 1 dependent.
MOfinder: A Novel Algorithm for Detecting Overlapping Modules from Protein-Protein Interaction Network

Since organism development and many critical cell biology processes are organized in modular patterns, many algorithms have been proposed to detect modules. In this study, a new method, MOfinder, was developed to detect overlapping modules in a protein-protein interaction (PPI) network. We demonstrate that our method is more accurate than other 5 methods. Then, we applied MOfinder to yeast and human PPI network and explored the overlapping information. Using the overlapping modules of human PPI network, we constructed the module-module communication network. Functional annotation showed that the immune-related and cancer-related proteins were always together and present in the same modules, which offer some clues for immune therapy for cancer. Our study around overlapping modules suggests a new perspective on the analysis of PPI network and improves our understanding of disease.
Comparison of lower extremity EMG between the 2-leg squat and modified single-leg squat in female athletes.

PURPOSE To compare EMG activity of selected hip and knee muscle groups in female athletes performing a modified single-leg squat and the 2-leg squat using the same relative intensity. METHODS Eleven Division I female athletes from a variety of sports (soccer, softball, and track) completed the study. EMG measurements were taken as the subjects completed 3 parallel repetitions at 85% of their 3-repetition maximum on each exercise. Mean and mean peak EMG data from the gluteus medius, hamstrings, and quadriceps and the quadriceps:hamstrings EMG ratio were compared between the 2 exercises. RESULTS Statistically higher mean (P < .01) and mean peak (P < .05) gluteus medius and mean and mean peak (P < .01) hamstring EMG activity occurred during the modified single-leg squat. The 2-leg squat produced higher mean and mean peak (P < .05) quadriceps activity and a higher quadriceps:hamstrings EMG ratio (P < .01). CONCLUSION Muscle-recruitment patterns appear to differ between the 2 types of squat exercises when performed at the same relative intensity by female athletes.
Specific gravity as an alternative to creatinine for estimating urine concentration in captive and wild chimpanzee (Pan troglodytes) Samples

The measurement of hormones in urine has become a widely used technique in primatology. Because urine concentration varies according to fluid intake, concentration must be measured in each sample collected, and hormone values are always expressed per unit of concentration. Traditionally, creatinine has been used as a concentration index, but some studies in humans have shown that creatinine varies among populations and even within and between individuals within a population, and that it begins to degrade after just one freeze–thaw cycle. In addition, creatinine measurement is relatively time‐consuming and expensive and creates hazardous waste. In this study, we tested the hypothesis that specific gravity, or the ratio of the density of a sample to that of water, is highly correlated with creatinine measurement in urine samples collected from captive chimpanzees at the New Iberia Research Center in Louisiana and wild chimpanzees at the Ngogo study site in the Kibale National Park, Uganda. We found that specific gravity and creatinine were highly correlated in both captive (N=124) and wild (N=13) chimpanzee samples, and that specific gravity measurement was robust to actual and simulated transport conditions and repeated freeze–thaw cycles. We recommend that researchers consider specific gravity measurement as a preferable alternative to creatinine measurement in their studies of primate endocrinology. Am. J. Primatol. 71:130–135, 2009. © 2008 Wiley‐Liss, Inc.
Distilling the ingredients of P2P live streaming systems

Peer-to-peer live streaming systems involve complex engineering and are difficult to test and to deploy. To cut through the complexity, we advocate such systems be designed by composing ingredients: a novel abstraction denoting the smallest interoperable units of code that each express a single design choice. We present a system, STREAMAID, that provides tools for designing protocols in terms of ingredients, systematically testing the impact of every design decision in a simulator, and deploying them in a wide-area testbed such as PlanetLab for evaluation. We show how to decompose popular P2P live streaming systems, such as CoolStreaming, BitTorrent Live and others, into ingredients and how STREAMAID can help optimize and adapt these protocols. By experimenting with the essential building blocks of which P2P live streaming protocols are comprised, we gain a unique vantage point of their relative quality, their bottlenecks and their potential for future improvement.
Why Are Online Catalogs Still Hard to Use?

We return to arguments made 10 years ago (Borgman, 1986a) that online catalogs are difficult to use because their design does not incorporate sufficient understanding of searching behavior. The earlier article examined studies of information retrieval system searching for their implications for online catalog design; this article examines the implications of card catalog design for online catalogs. With this analysis, we hope to contribute to a better understanding of user behavior and to lay to rest the card catalog design model for online catalogs. We discuss the problems with query matching systems, which were designed for skilled search intermediaries rather than end‐users, and the knowledge and skills they require in the information‐seeking process, illustrated with examples of searching card and online catalogs. Searching requires conceptual knowledge of the information retrieval process—translating an information need into a searchable query; semantic knowledge of how to implement a query in a given system—the how and when to use system features; and technical skills in executing the query—basic computing skills and the syntax of entering queries as specific search statements. In the short term, we can help make online catalogs easier to use through improved training and documentation that is based on information‐seeking behavior, with the caveat that good training is not a substitute for good system design. Our long term goal should be to design intuitive systems that require a minimum of instruction. Given the complexity of the information retrieval problem and the limited capabilities of today's systems, we are far from achieving that goal. If libraries are to provide primary information services for the networked world, they need to put research results on the information‐seeking process into practice in designing the next generation of online public access information retrieval systems. © 1996 John Wiley & Sons, Inc.
Multi-path transport over heterogeneous wireless networks: Does it really pay off?

Multi-path transfer protocols such as Concurrent Multi-Path Transfer for SCTP and Multi-Path TCP (MPTCP), are becoming increasingly popular, due to widespread deployment of smartphones with multi-homing support. Although the idea of using multiple interfaces simultaneously to improve application throughput is tempting, does transmission over multiple interfaces always provide benefits especially in realistic setup? In this paper, we first show that multi-path transfer might actually have a negative impact in real-world scenarios with mobile broadband and wireless LAN networks. We then introduce our Dynamic Relative Path Scoring (DRePaS) algorithm that continuously evaluates the contribution of paths to the overall performance and dynamically influences the scheduling decisions to make best use of the paths for the overall system performance. We show that DRePaS outperforms the current MPTCP implementation in terms of throughput and application delay, especially when the links are heterogeneous.
Early prosthetic joint infections treated with debridement and implant retention

Background and purpose Debridement and retention of the prosthesis is often attempted to treat early prosthetic joint infection (PJI). However, previous studies have found inconsistent results, with success rates ranging from 21% to 100%, and little has been written in the literature about hip function. We have therefore analyzed the clinical and functional outcome of early PJIs treated with this procedure. Patients and methods 38 patients with early PJI after primary hip arthroplasty who were treated with debridement and retention of the implant between 1998 and 2005 were studied prospectively, with a median follow-up time of 4 (0.8–10) years. Early infection was defined as that which occurred within 4 weeks of index arthroplasty. The primary outcome measure was infection control. Functional outcome was assessed with the Harris hip score. Results 27 of 38 patients were successfully treated, with no signs of infection or continued antibiotic treatment at the latest follow-up. Median Harris hip score was 86 (47–100) points. In 9 of the 11 patients for whom treatment failed, infection was successfully treated with 1-stage or 2-stage reimplantation or resection. Intraoperative cultures were positive in 36 hips, and the most frequently isolated organisms were Staphylococcus aureus and coagulase-negative staphylococci (CoNS). 15 infections were polymicrobial, and only 8 of them were successfully treated with debridement and retention of the implant. Interpretation Our data suggest that debridement and retention of the prosthesis is a reasonable treatment option in early PJI after primary hip arthroplasty, with satisfactory functional results.
Treatment for obstructive sleep apnoea: effect on peripheral nerve function

Background and objective: Obstructive sleep apnoea (OSA) is suggested to be associated with peripheral nerve damage. A case–control study was conducted to provide further support to this observation. In a longitudinal intervention study, it was examined whether treatment for OSA has a possible beneficial effect on peripheral nerve function. Methods: Participants were 23 patients with OSA and 23 controls matched for age and body mass index (BMI), all without any known cause of peripheral nerve damage. The sensory nerve action potential (SNAP) amplitudes of both sural nerves were determined. After 6 months of treatment for OSA, treatment compliance was evaluated and nerve conduction studies were repeated. Results: Patients with OSA had significantly lower mean (standard deviation) sural SNAP amplitudes than controls (6.3 (3.5) v 11.2 (5.0), p<0.001). Multivariate regression analysis including the variables age, BMI and Apnoea–Hypopnea Index (AHI) showed that both age (p<0.01) and AHI (p<0.05) were inversely related to the SNAP amplitude. On follow-up, the sural SNAP showed an increase of 2.6 mV on average (p<0.001). Multivariate regression analysis including the variables age, BMI, AHI, pretreatment SNAP and treatment compliance identified only treatment compliance as being significantly related to the SNAP increase (p⩽0.005). Conclusion: OSA is an independent risk factor for axonal dysfunction of peripheral sensory nerves. Impaired neural function is at least partly reversible with treatment for sleep apnoea.
A model-theoretic counterpart to Moishezon morphisms

In this note a natural strengthening of internality motivated by complex geometry, being "Moishezon" to a set of types, is introduced. Under the hypothesis of Pillay's canonical base property, and using results of Chatzidakis, a criterion is given for when a finite U-rank stationary type that is internal to a nonmodular minimal type is in fact Moishezon to the set of all nonmodular minimal types. This result is a model-theoretic analogue of (a special case of) Campana's "first algebraicity criterion". Other related abstractions from complex geometry, including "coreductions" and "generating fibrations" are also discussed.
Activation of Caspase‐3 in Developmental Models of Programmed Cell Death in Neurons of the Substantia Nigra

Abstract: Programmed cell death has been proposed to play a role in the death of neurons in acute and chronic degenerative neurologic disease. There is now evidence that the caspases, a family of cysteine proteases, mediate programmed cell death in various cells. In neurons, caspase‐3 (CPP32/Yama/apopain), in particular, has been proposed to play a role. We examined the expression of caspase‐3 in three models of programmed cell death affecting neurons of the substantia nigra in the rat: natural developmental neuron death and induced developmental death following either striatal target injury with quinolinic acid or dopamine terminal lesion with intrastriatal injection of 6‐hydroxydopamine. Using an antibody to the large (p17) subunit of activated caspase‐3, we have found that activated enzyme is expressed in apoptotic profiles in all models. Increased p17 immunostaining correlated with increased enzyme activity. The sub‐cellular distribution of activated caspase‐3 differed among the models: In natural cell death and the target injury model, it was strictly nuclear, whereas in the toxin model, it was also cytoplasmic. We conclude that p17 immunostaining is a useful marker for programmed cell death in neurons of the substantia nigra.
A Mixed-Methods Approach to Disclose the Influence of Twofold Information Usefulness on Sales

In the current study, we examine the relative effects of the two types of consumer reviews (i.e., Positive and negative eWOM) on consumers' purchase decisions, and the moderating roles of the two types of information usefulness (i.e., Explicit usefulness and implicit usefulness). Analyzing a large-scale panel data collected from an online shopping site, we found that consumers' purchase decisions are indeed influenced by both positive and negative reviews. In addition, a SVM classifier is built to identify the implicit useful reviews. Our results show that information usefulness, including explicit and implicit useful information, has an important moderating role in consumers' purchase decisions. This study contributes to the existing literature by explaining how information usefulness (i.e., Explicit and implicit usefulness) moderates the influence of consumer review on consumers' purchase decisions, and providing a classifier for consumer reviews through sentiment analysis in online social shopping sites. The results offer important and interesting insights to IS research and practice.
Holes Effects in Plane Periodic Multilayered Viscoelastic Media

This work deals with the study of the reflection and transmission properties of plane periodic structures composed of N periods (1 ≤ N ≤ 3) in the MHz frequency range. The period consists of two bounded plates presenting a high acoustic impedance contrast one of which is in aluminum, the other is in polyethylene. The longitudinal and transversal attenuations are considered in polyethylene and neglected in aluminum. We take into account the case of emerging holes in the polyethylene layer. Simulations are based on the stiffness matrix method (SMM) developed by Rokhlin. When attenuation is considered in polyethylene, the reflection coefficients are different depending on the insonification side. The comparison of results without or with holes configurations are performed and showed that throughout holes allow the rapid observation of forbidden bands. The attenuation of the whole multilayer is also determined.
Glycine bidirectionally regulates ischemic tolerance via different mechanisms including NR2A‐dependent CREB phosphorylation

The exact effect of glycine pre‐treatment on brain ischemic tolerance (IT) remains quite controversial. The objective of this study was to investigate the potential effects of glycine on IT. We used rat models of both in vitro ischemia (oxygen and glucose deprivation) and in vivo ischemia (transient middle cerebral artery occlusion). Low doses of glycine (L‐Gly) significantly decreased hippocampal ischemic LTP (i‐LTP), infarct volume, and neurological deficit scores which were administered before ischemia was induced in rats, whereas high doses of glycine exerted deteriorative effects under the same condition. These findings suggested that exogenous glycine may induce IT in a dose‐dependent manner. Furthermore, L‐Gly‐dependent neuronal protection was inversed by L689, a selective NMDAR glycine site antagonist both in vitro (abolished i‐LTP depression) and in vivo (increased infarct size reduction), but not glycine receptor (GlyR) inhibitor strychnine. Importantly, L‐Gly‐induced IT was achieved by NR2A‐dependent cAMP‐response element binding protein phosphorylation. These data imply that glycine pre‐treatment may represent a novel strategy for inducing IT based on synaptic NMDAR‐dependent neuronal transmission.
The Mediterranean diet: health, science and society

The Mediterranean diet (MD) emerged as a healthy food regimen long before it could be recognised which nutrients or foods were responsible for its observed benefits, and it was only in the middle of the last century that the first scientific approach ‘The Seven Countries Study’ appeared. Epidemiological and anthropological studies of the MD converged, first by investigating at single nutrients or foods, then by adopting the more holistic approach of dietary patterns (DP), and now with a molecular approach. These studies resulted in convincing evidence that a MD decreases the risk of all-cause mortality and cardiovascular mortality and incidence. A risk reduction of developing type 2 diabetes is probable. Evidence is less stringent for other metabolic diseases and all cancers but from possible to probable for some cancer sites. Although DP showed that the MD has to be considered in its totality, olive oil could have a specific role. Lifestyle factors such as physical activity for energy balance, outdoor life for vitamin D synthesis and conviviality are also probably partly responsible for the health benefits. The MD is a lifestyle well suited for coping not only with personal health but also with wider societal concerns in relation to environment, public health and economy.