Miracle-dz/UniFAR-FTUs huggingface dataset:
Sex-specific metabolic interactions between liver and adipose tissue in MCD diet-induced non-alcoholic fatty liver disease

Higher susceptibility to metabolic disease in male exemplifies the importance of sexual dimorphism in pathogenesis. We hypothesized that the higher incidence of non-alcoholic fatty liver disease in males involves sex-specific metabolic interactions between liver and adipose tissue. In the present study, we used a methionine-choline deficient (MCD) diet-induced fatty liver mouse model to investigate sex differences in the metabolic response of the liver and adipose tissue. After 2 weeks on an MCD-diet, fatty liver was induced in a sex-specific manner, affecting male mice more severely than females. The MCD-diet increased lipolytic enzymes in the gonadal white adipose tissue (gWAT) of male mice, whereas it increased expression of uncoupling protein 1 and other brown adipocyte markers in the gWAT of female mice. Moreover, gWAT from female mice demonstrated higher levels of oxygen consumption and mitochondrial content compared to gWAT from male mice. FGF21 expression was increased in liver tissue by the MCD diet, and the degree of upregulation was significantly higher in the livers of female mice. The endocrine effect of FGF21 was responsible, in part, for the sex-specific browning of gonadal white adipose tissue. Collectively, these data demonstrated that distinctively female-specific browning of white adipose tissue aids in protecting female mice against MCD diet-induced fatty liver disease.
Variability in the Location of the Retinal Ganglion Cell Area Centralis Is Correlated with Ontogenetic Changes in Feeding Behavior in the Black Bream, Acanthopagrus butcheri (Sparidae, Teleostei)

The development of neural cell topography in the retinal ganglion cell layer was examined in a teleost, the black bream (Acanthopagrus butcheri). From Nissl-stained wholemounts, it was established that fish between 10 and 15 mm standard body length (SL) possess high cell densities throughout the dorso-temporal retinal quadrant, with peak cell densities located in temporal regions of the retina. However, in fish between 15 and 80 mm SL, a wide variation in the position of the peak cell density is revealed with the locations of the areae centrales (AC) ranging from exclusively temporal to periphero-dorsal retina. Fish larger than 80 mm SL always possess an AC located in the dorsal region of the dorso-temporal retinal quadrant. The topography of ganglion cells within the ganglion cell layer was determined by comparing the numbers of ganglion cells retrogradely-labeled from the optic nerve with the total population of Nissl-stained neurons (ganglion plus displaced amacrine cells) in a range of different-sized individuals. Ganglion cell topography was the same as that recorded for all Nissl-stained neurons. The feeding behavior of juveniles from metamorphosis to 80 mm SL was observed, where fish were given the choice of feeding on live food in mid-water (until 15 mm SL) or obtaining pellets from the surface or the bottom. A range of feeding patterns was recorded, with the smallest fish taking food from mid-water but individuals between 15 and 80 mm SL taking food either from the surface or the bottom or both. A correlation between the preferred mode of feeding and the position of the AC was found, such that those individuals feeding in mid-water or at the surface possess a temporal or intermediate (dorso- temporal) AC, whereas those predominantly feeding from the bottom possess a dorsal AC.
Conceptual Processing during the Conscious Resting State: A Functional MRI Study

Localized, task-induced decreases in cerebral blood flow are a frequent finding in functional brain imaging research but remain poorly understood. One account of these phenomena postulates processes ongoing during conscious, resting states that are interrupted or inhibited by task performance. Psychological evidence suggests that conscious humans are engaged almost continuously in adaptive processes involving semantic knowledge retrieval, representation in awareness, and directed manipulation of represented knowledge for organization, problem-solving, and planning. If interruption of such conceptual processes accounts for task-induced deactivation, tasks that also engage these conceptual processes should not cause deactivation. Furthermore, comparisons between conceptual and nonconceptual tasks should show activation during conceptual tasks of the same brain areas that are deactivated relative to rest. To test this model, functional magnetic resonance imaging data were acquired during a resting state, a perceptual task, and a semantic retrieval task. A network of left-hemisphere poly-modal cortical regions showed higher signal values during the resting state than during the perceptual task but equal values during the resting and semantic conditions. This result is consistent with the proposal that perceptual tasks interrupt processes ongoing during rest that involve many of the same brain areas engaged during semantic retrieval. As further evidence for this model, the same network of brain areas was activated in two direct comparisons between semantic and perceptual processing tasks. This same conceptual processing network was also identified in several previous studies that contrasted semantic and perceptual tasks or resting and active states. The model proposed here offers a unified account of these findings and may help to explain several unanticipated results from prior studies of semantic processing.
Late Life Function and Disability Instrument: II. Development and evaluation of the function component.

BACKGROUND Self-reported capability in physical functioning has long been considered an important focus of research for older persons. Current measures have been criticized, however, for conceptual confusion, lack of sensitivity to change, poor reproducibility, and inability to capture a wide range of upper and lower extremity functioning. METHODS Using Nagi's disablement model, we wrote physical functioning questionnaire items that assessed difficulty in 48 common daily tasks. We constructed the instrument using factor analysis and Rasch analytic techniques and evaluated its validity and test-retest reliability with 150 ethnically and racially diverse adults aged 60 years and older who had a range of functional limitations. RESULTS Our analyses resulted in a 32-item function component with three dimensions--upper extremity, basic lower extremity, and advanced lower extremity functions. Expected differences in summary scores of known-functional limitation groups support its validity. Test-retest stability over a 1- to 3-week period was extremely high (intraclass correlation coefficients =.91 to.98). CONCLUSIONS The Late-Life Function and Disability Instrument has potential to assess activity concepts related to upper and lower extremity functioning across a wide variety of daily physical tasks and individual levels of physical functioning.
DEG/ENaC channels: A touchy superfamily that watches its salt

To the surprise of many, studies of molecular mechanisms of touch transduction and analyses of epithelial Na+ transport have converged to define a new class of ion channel subunits. Based on the names of the first two identified subfamilies, the Caenorhabditis elegans degenerins and the vertebrate epithelial amiloride‐sensitive Na+ channel, this ion channel class is called the DEG/ENaC superfamily. Members of the DEG/ENaC superfamily have been found in nematodes, flies, snails, and vertebrates. Family members share common topology, such that they span the membrane twice and have intracellular N‐ and C‐termini; a large extracellular loop includes a conserved cysteine‐rich region. DEG/ENaC channels have been implicated a broad spectrum of cellular functions, including mechanosensation, proprioception, pain sensation, gametogenesis, and epithelial Na+ transport. These channels exhibit diverse gating properties, ranging from near constitutive opening to rapid inactivation. We discuss working understanding of DEG/ENaC functions, channel properties, structure/activity correlations and possible evolutionary relationship to other channel classes. BioEssays 21:568–578, 1999. © 1999 John Wiley & Sons, Inc.
Ekstazi: Lightweight Test Selection

Regression testing is a crucial, but potentially time-consuming, part of software development. Regression test selection (RTS), which runs only a subset of tests, was proposed over three decades ago as a promising way to speed up regression testing. However, RTS has not been widely adopted in practice. We propose EKSTAZI , a lightweight RTS tool, that can integrate well with testing frameworks and build systems, increasing the chance for adoption. EKSTAZI tracks dynamic dependencies of tests on files and requires no integration with version-control systems. We implemented EKSTAZI for Java+JUnit and Scala+ScalaTest, and evaluated it on 615 revisions of 32 open-source projects (totaling almost 5M LOC). The results show that EKSTAZI reduced the end-to-end testing time by 32% on average compared to executing all tests. EKSTAZI has been adopted for day-to-day use by several Apache developers. The demo video for EKSTAZI can be found at http://www.youtube. com/watch? v=jE8K5_UCP28.
FIRM: Flow-based Interference-aware Route Management in Wireless Mesh Networks

In IEEE 802.11-based wireless mesh networks, routing is crucial in achieving high throughput in face of both interflow and intra-flow interference. Prior work focuses on finding the maximum available bandwidth path when a new flow enters the network. However, few has considered the effect of the new flow on the throughput of the existing flows. We propose a routing framework that uses the topology map of a mesh network with the carrier sense and interference relations and estimates the available bandwidth of a candidate path. We propose two algorithms for finding a route for a new flow: (1) FIRM searches for the maximum bandwidth path for the new flow, and (2) FIRM + not only considers the available bandwidth of a path for the new flow, but also the amount of throughput degradation of existing flows. We implement and evaluate FIRM and FIRM + with the IRU routing algorithm on a 15 node indoor IEEE 802.11a testbed. Various experiments reveal that FIRM + achieves the highest total throughput of all flows.
Silicon defects in diamond.

Synthetic diamonds have been grown from metal melts containing silicon, at high pressures and high temperatures. The absorption and photoluminescence spectra have been investigated in the temperature range 1.8--77 K. A 12-line fine structure is observed close to 1.682 eV, and this can be divided into three similar groups each containing four components. The relative strengths of the optical absorption for the three groups of lines are found to be the same as the ratio of the abundancies of the natural isotopes of silicon, $^{28}\mathrm{Si}$, $^{29}\mathrm{Si}$, and $^{30}\mathrm{Si}$, thus showing that the 1.682-eV center is related to silicon impurity. The changes in the relative intensities of the four component lines associated with $^{28}\mathrm{Si}$ indicate that the center has two ground-state energy levels with a separation of 0.20 meV. The occupancies of the two excited-state levels of separation 1.07 meV tend to reach thermal equilibrium after optical excitation and before luminescence takes place. The relative transition probabilities for the transitions have been determined. The degeneracies of the ground-state levels are the same, and the degeneracies of the excited-state levels are also equal to one another. The behavior of the 1.682-eV defect after electron irradiation and subsequent heat treatment is described.
Extraction and deproteinization of pumpkin polysaccharide

Extraction and deproteinization methods of polysaccharide from pumpkin were studied. We extracted crude polysaccharide by the method of hot water extraction. The percentages of deproteinization and polysaccharide loss were compared as indexes using the trichloroacetic acid (TCA) method, the NaCl method, the and CaCl2 method, respectively. The results showed that the TCA method exhibited the lowest percentage of deproteinization, and a little higher percentage of polysaccharide loss than the other two methods. The CaCl2 method excelled over the NaCl method in deproteinization.
Selection and classification of gene expression in autism disorder: Use of a combination of statistical filters and a GBPSO-SVM algorithm

In this work, gene expression in autism spectrum disorder (ASD) is analyzed with the goal of selecting the most attributed genes and performing classification. The objective was achieved by utilizing a combination of various statistical filters and a wrapper-based geometric binary particle swarm optimization-support vector machine (GBPSO-SVM) algorithm. The utilization of different filters was accentuated by incorporating a mean and median ratio criterion to remove very similar genes. The results showed that the most discriminative genes that were identified in the first and last selection steps included the presence of a repetitive gene (CAPS2), which was assigned as the gene most highly related to ASD risk. The merged gene subset that was selected by the GBPSO-SVM algorithm was able to enhance the classification accuracy.
The Homotopy Perturbation Method for Solving K(2,2) Equation

In this paper, we present homotopy perturbation method (HPM) for solving the Korteweg-de Vries (KdV) equation and convergence study of homotopy perturbation method for nonlinear partial differential equation. We compared our solution with the exact solution and homotopy analysis method (HAM). The results show that the HPM is an appropriate method for solving nonlinear equation.
A Survey on LDPC Codes and Decoders for OFDM-based UWB Systems

Current UWB systems apply convolutional codes as their channel coding scheme. For next generation systems LDPC codes are in discussion due to their outstanding communications performance. LDPC codes are already utilized in the new WiMax and WiFi standards. Thus it is reasonable to investigate these codes as candidate LDPC codes for UWB. In this paper the authors present an implementation complexity and performance comparison of LDPC decoders. We will show that it is of great advantage to design new LDPC codes which are tailored to the special latency and throughput constraints of upcoming UWB systems. This new class of LDPC codes is named ultra-sparse LDPC codes. Synthesis results of WiMax, WiFi, and U-S LDPC decoders are presented based on an enhanced 65 nm CMOS process. We show that the implementation complexity of the new U-S LDPC decoders is 55% smaller, utilizing only 0.2 mm2 instead of over 0.4 mm2, while the communications performance of all observed LDPC codes are almost identical under all the considered UWB simulation conditions.
Occupational therapy students in the process of interprofessional collaborative learning: A grounded theory study

The purpose of this grounded theory study was to generate a theory of the interprofessional collaborative learning process of occupational therapy (OT) students who were engaged in a collaborative learning experience with students from other allied health disciplines. Data consisted of semi-structured interviews with nine OT students from four different interprofessional collaborative learning experiences at three universities. The emergent theory explained OT students' need to build a culture of mutual respect among disciplines in order to facilitate interprofessional collaborative learning. Occupational therapy students went through a progression of learned skills that included learning how to represent the profession of OT, hold their weight within a team situation, solve problems collaboratively, work as a team, and ultimately, to work in an actual team in practice. This learning process occurred simultaneously as students also learned course content. The students had to contend with barriers and facilitators that influenced their participation and the success of their collaboration. Understanding the interprofessional learning process of OT students will help allied health faculty to design more effective, inclusive interprofessional courses.
On Rationality of Nonnegative Matrix Factorization

Nonnegative matrix factorization (NMF) is the problem of decomposing a given nonnegative n × m matrix M into a product of a nonnegative n × d matrix W and a nonnegative d × m matrix H. NMF has a wide variety of applications, including bioinformatics, chemometrics, communication complexity, machine learning, polyhedral combinatorics, among many others. A longstanding open question, posed by Cohen and Rothblum in 1993, is whether every rational matrix M has an NMF with minimal d whose factors W and H are also rational. We answer this question negatively, by exhibiting a matrix M for which W and H require irrational entries. As an application of this result, we show that state minimization of labeled Markov chains can require the introduction of irrational transition probabilities. We complement these irrationality results with an NP-complete version of NMF for which rational numbers suffice.
Efficacy of an Educational and Counseling Intervention on Adherence to Highly Active Antiretroviral Therapy: French Prospective Controlled Study

Abstract Purpose: The objective was to evaluate the impact of an intervention for improving adherence to antiretroviral therapies (HAART) in HIV-infected patients. Method: We designed a prospective, controlled, randomized trial to assess the impact of an educational and counseling intervention in addition to standard of care. At M0, the study enrolled 244 HAART-treated patients who attended a medical consultation between September and December 1999 who were not included in another protocol. Patients in the intervention group (IG) were offered three individual sessions by trained nurses. The proportions of adherent patients at 6 months followup (M6) and the change in HIV RNA between M0 and M6 were measured. Results: Between M0 and M6, HIV RNA significantly decreased in the 123 patients of the IG (mean difference = –0.22 log [±0.86], p = .013), while it increased (+0.12 log [±0.90], p = .14) in the 121 patients of the control group. However, the proportion of patients with HIV RNA <40 copies/mL remained similar in both groups. In an intent-to-treat analysis, the only significant predictor of 100% adherence at M6 was the intervention group (p = .05) after adjustment for baseline adherence (p = .001). Among the 202 patients with available data on adherence, the proportion of adherent patients was similar in both groups at M0 (58% vs. 63%, p = .59) but became higher in the IG at M6 (75% vs. 61%, p = .04). Conclusion: The educational and counseling intervention was efficient for increasing adherence to HAART and could be implemented in most clinical settings.
Performance Analysis on Spectral-Energy Efficiency Tradeoff in the D2D-Relay Mechanism

The D2D-Relay mechanism, which integrates device-to- device (D2D) communications and relay technology, is promising in system performance improvement. This paper focuses on studying what kind of benefits the D2D-Relay mechanism could bring into a wireless communication system during the uplink transmission. To comprehensively analyze the system performance, we use a metric, which consists of the spectral efficiency (SE) and the energy efficiency (EE), as an indicator. With this criteria in mind, we theoretically describe the influence from users' preferences to the SE and the EE in detail. Noting that user pairing is an important part of this mechanism, we evaluate the performance of the D2D- Relay mechanism with three typical pairing algorithms based on different criteria. The simulation results conform to our derivations and reveal the performance gain brought by applying the D2D-Relay mechanism. In addition, with different configurations of the number of the users and their preferences to the SE and the EE, the most appropriate algorithm is suggested for the practical application.
On application of LASSO for sparse support recovery with imperfect correlation awareness

In this paper, the problem of identifying the common sparsity support of multiple measurement vectors (MMV) is considered. The model is given by y[n] = Ax<sub>s</sub>[n], 1 ≤ n ≤ L where {y[n]}<sub>n=1</sub><sup>L</sup> denote the L measurement vectors, A ∈ R<sup>M×N</sup> is the measurement matrix and x<sub>s</sub>[n] ∈ R<sup>N</sup> are the unknown vectors with same sparsity support denoted by the set S<sub>0</sub> with |S<sub>0</sub>| = D. It has been shown in a recent paper by the authors that when the elements of x<sub>s</sub>[n] are uncorrelated from each other, one can recover sparsity levels as high as O(M<sup>2</sup>) for suitably designed measurement matrix. This result was shown assuming the knowledge that the nonzero elements are perfectly uncorrelated and that we have perfect estimates for the data correlation matrix, (the latter is true in the limit as L → ∞). In this paper, we formulate the problem of support recovery in the non ideal setting, i.e., when the correlation matrix is estimated with finite L. The resulting support recovery problem which explicitly utilizes the correlation knowledge, can be formulated as a LASSO. The performance of such “correlation aware” LASSO is analyzed by providing lower bounds on the probability of successful recovery as a function of the number L of measurement vectors. Numerical results are also provided to demonstrate the superior performance of the proposed correlation aware framework over conventional MMV techniques under identical conditions.
Clathrin‐Dependent or Not: Is It Still the Question?

Whether the endocytic uptake of a given molecule is mediated through clathrin‐coated pits or not is a classical criterion used to characterize its endocytic pathway(s). Hence, clathrin‐dependent endocytosis has been associated with highly selective and efficient uptake, whereas clathrin‐independent endocytosis appeared to be confined to bulk uptake of fluid‐phase markers. This scholastic view has recently been challenged using newly developed molecular tools that allow for the first time a functional and mechanistic analysis of these less well‐characterized clathrin‐independent pathways, including caveolar uptake and macropinocytosis. Furthermore, several studies point to a critical role of lateral lipid asymmetry – lipid rafts/microdomains – in membrane sorting. We will discuss the potential role of these structures in endocytosis and the possibility that differential sorting at the plasma membrane predisposes the ensuing intracellular fate of a given molecule as well as its physiological function.
Eukaryote Culturomics of the Gut Reveals New Species

The repertoire of microeukaryotes in the human gut has been poorly explored, mainly in individuals living in northern hemisphere countries. We further explored this repertoire using PCR-sequencing and culture in seven individuals living in four tropical countries. A total of 41 microeukaryotes including 38 different fungal species and three protists were detected. Four fungal species, Davidiella tassiana, Davidiella sp. , Corticiaceae sp. , and Penicillium sp. , were uniquely detected by culture; 27 fungal species were uniquely detected using PCR-sequencing and Candida albicans, Candida glabrata, Trichosporon asahii, Clavispora lusitaniae, Debaryomyces hansenii, Malassezia restricta, and Malassezia sp. were detected using both molecular and culture methods. Fourteen microeukaryotes were shared by the seven individuals, whereas 27 species were found in only one individual, including 11 species in Amazonia, nine species in Polynesia, five species in India, and two species in Senegal. These data support a worldwide distribution of Malassezia sp. , Trichosporon sp. , and Candida sp. in the gut mycobiome. Here, 13 fungal species and two protists, Stentor roeseli and Vorticella campanula, were observed for first time in the human gut. This study revealed a previously unsuspected diversity in the repertoire of human gut microeukaryotes, suggesting spots for further exploring this repertoire.