Miracle-dz/UniFAR-FTUs huggingface dataset:
Theoretical developments in the study and prediction of food intake

The purpose of the present paper is to review recent theoretical developments in food intake modelling applied to animal science and ecology. The models are divided into those that have been developed for intensive agricultural systems, and those which consider more extensive systems and natural systems. For the most part the present paper discusses models that predict the food intake of herbivores. The mechanisms of each model are discussed, along with a brief mention of the experimental support for the most popular models. We include a discussion of models that approach the study of food intake behaviour from an evolutionary perspective, and suggest that lifetime models are especially useful when food intake carries an intrinsic cost. These long timescale evolutionary models contrast with the more common food intake models, whose timescale is usually much shorter. We conclude that the ‘eating to requirements’ model highlights an important food intake mechanism that provides an accurate predictive tool for intensive agricultural systems. The mechanisms of food intake regulation in extensive systems are less certain, and closer links between the ideas of animal science and ecology will be helpful for improving our understanding of food intake regulation.
Comparison of Alternative Coupling Methods of the Vibrant Soundbridge Floating Mass Transducer

The active middle ear implant Vibrant Soundbridge© provides a variety of coupling modalities of the floating mass transducer (FMT) to various structures of the ossicular chain and the round window. A retrospective analysis was performed on 125 subjects (n = 137 ears) (1) to compare the efficacy of the different FMT coupling modalities with increasing degree of hearing loss, (2) to compare the performance in speech outcome and the effective gain between the coupling types, and (3) to evaluate the risk of additional hearing loss of each coupling procedure. The patients were grouped according to their type of FMT coupling into incus vibroplasty (incus group, n = 59), round window vibroplasty with coupler (RWC group, n = 23), round window vibroplasty without coupler (RW group, n = 22), and oval window vibroplasty with coupler (OWC group, n = 33). For each coupling group, pre- and postoperative thresholds, the results of the Freiburg monosyllable test at 65 dB SPL, and the effective gain across frequencies (0.5-6 kHz) were evaluated. A logistic regression function was used to describe the relationship between word recognition scores (WRS, in % correct) and the mean bone conduction (BC) hearing loss. The surgical procedure had no clinically relevant effect on BC thresholds of patients in each coupling group. The BC pure tone average (PTA4) for 50% WRS predicted by the model function was similar for the incus (48.2 dB nHL), RW (47.8 dB nHL), and OWC (49.0 dB nHL) groups, but higher for the RWC group (67.9 dB nHL). However, the median WRS was 80% or better with no significant differences in speech perception between coupling types (Kruskal-Wallis test, p = 0.229). The effective gain shows an advantage for the incus coupling between 0.5 and 2 kHz over the other coupling types. The performance of the FMT coupling modalities is equally good for patients with a mild-to-moderate hearing loss, but the efficacy of coupling types differs for patients with greater hearing loss (>48 dB BC HL).
Nef Secretion into Extracellular Vesicles or Exosomes Is Conserved across Human and Simian Immunodeficiency Viruses

ABSTRACT Extracellular vesicles (EVs) or exosomes have been implicated in the pathophysiology of infections and cancer. The negative regulatory factor (Nef) encoded by simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV) plays a critical role in the progression to AIDS and impairs endosomal trafficking. Whether HIV-1 Nef can be loaded into EVs has been the subject of controversy, and nothing is known about the connection between SIV Nef and EVs. We find that both SIV and HIV-1 Nef proteins are present in affinity-purified EVs derived from cultured cells, as well as in EVs from SIV-infected macaques. Nef-positive EVs were functional, i.e., capable of membrane fusion and depositing their content into recipient cells. The EVs were able to transfer Nef into recipient cells. This suggests that Nef readily enters the exosome biogenesis pathway, whereas HIV virions are assembled at the plasma membrane. It suggests a novel mechanism by which lentiviruses can influence uninfected and uninfectable, i.e., CD4-negative, cells. IMPORTANCE Extracellular vesicles (EVs) transfer biologically active materials from one cell to another, either within the adjacent microenvironment or further removed. EVs also package viral RNAs, microRNAs, and proteins, which contributes to the pathophysiology of infection. In this report, we show that both human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) incorporate the virus-encoded Nef protein into EVs, including EVs circulating in the blood of SIV-infected macaques and that this presents a novel mechanism of Nef transfer to naive and even otherwise non-infectable cells. Nef is dispensable for viral replication but essential for AIDS progression in vivo. Demonstrating that Nef incorporation into EVs is conserved across species implicates EVs as novel mediators of the pathophysiology of HIV. It could help explain the biological effects that HIV has on CD4-negative cells and EVs could become biomarkers of disease progression. Extracellular vesicles (EVs) transfer biologically active materials from one cell to another, either within the adjacent microenvironment or further removed. EVs also package viral RNAs, microRNAs, and proteins, which contributes to the pathophysiology of infection. In this report, we show that both human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) incorporate the virus-encoded Nef protein into EVs, including EVs circulating in the blood of SIV-infected macaques and that this presents a novel mechanism of Nef transfer to naive and even otherwise non-infectable cells. Nef is dispensable for viral replication but essential for AIDS progression in vivo. Demonstrating that Nef incorporation into EVs is conserved across species implicates EVs as novel mediators of the pathophysiology of HIV. It could help explain the biological effects that HIV has on CD4-negative cells and EVs could become biomarkers of disease progression.
Health behaviors and obesity among Hispanics with depression, United States 2006.

OBJECTIVE To examine the differences in health behaviors, and obesity between Hispanics and non-Hispanic Whites with depression. DESIGN Depression data were gathered from 38 states, the District of Columbia, Puerto Rico, and the US Virgin Islands using the 2006 Behavioral Risk Factor Surveillance System, a state-based random-digit-dialed telephone survey of adults aged > or =18 years (n=156,991). The Patient Health Questionnaire 8 was used to determine current depression. Lifetime diagnosis of depression was assessed by self-report of physician diagnosis. Prevalence ratios were calculated to examine the racial/ethnic differences in leisure-time physical activity, cigarette smoking, binge drinking, heavy drinking and obesity among people with current depression and lifetime diagnosis of depression. RESULTS There were significant differences in age, education, and health care coverage between Hispanics and non-Hispanic Whites with current depression and lifetime diagnosis of depression. Hispanics with current depression and with lifetime diagnosis of depression were more likely to be obese than non-Hispanic Whites. After adjusting for demographic factors, health care coverage, and self-rated health status, Hispanics with current depression were 17% more likely not to participate in leisure-time physical activity and 42% less likely to be a current cigarette smoker compared with non-Hispanic Whites. Hispanics with lifetime diagnosis of depression were 14% more likely not to participate in leisure-time physical activity and 44% less likely to be a current cigarette smoker than non-Hispanic Whites after adjusting for confounders. CONCLUSIONS Public health intervention programs are needed to promote healthy behaviors especially physical activity participation with in the Hispanic community, and paying particular attention to people who already are depressed.
CRITICAL REVIEW OF THE MODIFIED WINDING FUNCTION THEORY

The Modifled Winding Function Theory (MWFTh), regarded as a very powerful and general theory, has been extensively used for the last 15 years. This paper performs an in-depth review of the mathematical and physical framework on which the MWFTh is based, showing that it is indeed very well suited to analyse machines with small air gaps of arbitrary shape. However, contrary to what is usually stated in the literature, it is also proved that its general formulae fail when applied to large air gaps. This major flnding is deduced from two difierent approaches, both of which are later reinforced by numerical examples. In spite of that, there is an important industrial fleld (diagnosis techniques of salient-pole synchronous machines eccentricities) in which good theoretical results have been reported by applying the MWFTh to these large air-gap machines. This issue is addressed and clarifled in the paper.
Glutamine and glutaminolysis are required for efficient replication of infectious spleen and kidney necrosis virus in Chinese perch brain cells

Viruses rely on host cellular metabolism for energy and macromolecule synthesis during their replication. Infectious spleen and kidney necrosis virus (ISKNV) causes significant economic losses in the Chinese perch (Siniperca chuatsi) industry worldwide. However, little is known about the relationship between ISKNV replication and cellular metabolism. Using transcriptomic analysis, we observed that glutamine metabolism in Chinese perch brain (CPB) cells is altered during ISKNV infection. Moreover, ISKNV replication was decreased in CPB cells cultured in the glutamine-depleted medium. ISKNV replication was also inhibited in CPB cells cultured in the presence of bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl) ethyl sulfide (an inhibitor of glutaminase), (–)-epigallocatechinmo nogallate (an inhibitor of glutamate dehydrogenase) or L-buthionine sulfoximine (an inhibitor of glutathione synthesis). However, virus replication was rescued by the addition of multiple tricarboxylic acid cycle intermediates, ATP, or glutathione reduced ethyl ester. ATP and reduced glutathione/oxidized glutathione levels were increased in CPB cells infected with ISKNV, but were decreased in CPB cells cultured in glutamine-depleted medium. These results indicate ISKNV infection induces glutaminolysis to accommodate the biosynthetic and energy needs for its efficient virus replication.
Unpolished Thai Rice Prevents Aberrant Crypt Foci Formation through the Invovement of ?catenin and COX2 Expression in AzoxymethaneTreated Rats.

Colorectal cancer (CRC) is a major cause of morbidity and mortality throughout the world, with chronic inflammation and diet as major causes in its development. Chemopreventive effects of natural dietary products have been the focus of studies for prevention over the past decade. This study was conducted to determine the effects of unpolished Thai rice during precancerous stage through the involvement of ? catenin, cyclooxygenase2 (COX2) expression and inflammatory cytokines focusing on azoxymethane (AOM)induced aberrant crypt foci (ACF)related to CRC. Male Sprague Dawley rats received two injections of AOM (15 mg/kg body weight) at weeks 4 and 5 while rats were treated with 20% or 70% unpolished Thai rice. The rats were sacrificed at week 38 and the colons removed for aberrant crypt foci (ACF) identification. Histopathologic changes, immunohistochemical analysis of ? catenin and COX2 expression, and cytokine expression of proinflammatory and antiinflammatory markers were determined. The administration of unpolished Thai rice significantly and dose dependently decreased the total number of ACF and the percentages of ACF with highgrade dysplasia. Interestingly, unpolished Thai rice suppressed the expression of βcatenin and COX2. In addition, it also altered proinflammatory (IL6 and IFNγ) and antiinflammatory (IL 10) markers. The results suggested that unpolished Thai rice may provide a promising dietary intake for prevention during precancerous stage of CRC development, through the involvement of βcatenin and COX2 expression, and also modulate inflammatory cytokinesrelated to CRC.
Investigational immunosuppressants in early-stage clinical trials for the treatment of multiple sclerosis

ABSTRACT Introduction: Multiple sclerosis (MS) is a chronic demyelinating disease of the central nervous system with an immune mediated pathogenesis. Several therapies that suppress or modulate diverse immune system functions have been used for decades with the aim of modifying the disease course. However, these treatments have either limited efficacy or potentially serious adverse events that prevent first-line use on large scale. Areas covered: The aim of the present article is to review ongoing or recently completed clinical trials investigating immunosuppressive drugs for MS. The websites clinicaltrials.gov, clinicaltrialsregister.eu, and pubmed.gov were searched for phase 1, phase 2, and phase 3 trials starting from 2012. Twelve drugs were identified, including seven monoclonal antibodies and five small molecules. Expert opinion: Current or recently completed trials of immunosuppressants for MS are mainly proof-of-concept studies enrolling patients with relapsing disease and using efficacy endpoints based on magnetic resonance imaging measures of inflammatory activity. Sphingosine 1-phosphate receptor modulators and B-cell depleting therapies represent the most commonly investigated drugs, suggesting that mechanisms of action that have already shown promise for MS treatment are being exploited to find new therapies with improved safety, tolerability, and convenience of dosing. Clinical trials of immunosuppressants for progressive MS are largely lacking.
Gait Kinematic Deviations in Patients With Developmental Dysplasia of the Hip Treated With Total Hip Arthroplasty.

Comprehensive gait analysis of patients with Crowe type II and III developmental dysplasia of the hip (DDH) after successful total hip arthroplasty (THA) is lacking in the literature. This study evaluated gait function in joint kinematics after unilateral and bilateral THA in patients with DDH. In addition, the effect of high cup position on gait function was investigated. A total of 16 unilateral and 15 bilateral cementless THA patients due to DDH and 10 healthy participants comprised the study population. Levels of superior displacement of the acetabular cup and leg-length discrepancy after THA were measured. Three-dimensional gait analysis for patients who underwent THA was performed at least 1 year postoperatively. Range of motion (ROM), particularly sagittal (flexion/extension) and frontal (adduction/abduction) hip joint ROM, was significantly lower in both the unilateral and bilateral groups than in healthy participants. Sagittal (flexion/extension) hip ROM in patients with DDH was greater in the unilateral group than in the bilateral group. A significant influence of high acetabular cup position on hip joint kinematics was not observed in the unilateral subgroups (mean level of cup superior displacement was 11.8 mm). In contrast, a significant influence of high acetabular cup position on hip joint kinematics was observed in the bilateral subgroups (mean level of cup superior displacement was 21.3 mm). The functional symmetry and cup superior displacement within 12 mm in patients with DDH after unilateral THA contributed to the restoration of normal hip biomechanics. [Orthopedics. 2017; 40(3):e425-e431. ].
Dust in Resonant Extrasolar Kuiper Belts: Grain Size and Wavelength Dependence of Disk Structure

This paper considers the distribution of dust that originates in the breakup of planetesimals that are trapped in resonance with a planet. It is shown that there are three distinct grain populations with different spatial distributions: (I) large grains have the same clumpy resonant distribution as the planetesimals; (II) moderate-sized grains are no longer in resonance and have an axisymmetric distribution; and (III) small grains are blown out of the system by radiation pressure and so have a density distribution that falls off as τ ∝ 1/r. Population III can be further divided into two subclasses: (IIIa) grains produced from population I that exhibit trailing spiral structure that emanates from the resonant clumps and (IIIb) grains produced from population II that have an axisymmetric distribution. Since observations in different wavebands are sensitive to different dust sizes, multiwavelength imaging of debris disks can be used to test models that explain the submillimeter structure of debris disks as due to resonant trapping of planetesimals. For example, a collisional cascade without blowout grains would appear clumpy in the submillimeter (which samples population I) and smooth at mid- to far-IR wavelengths (which sample population II). The wavelength of transition from clumpy to smooth structure is indicative of the mass of the perturbing planet. The size distribution of Vega's disk is modeled showing that the large quantities of population III grains detected recently by Spitzer must originate in the destruction of the grains seen in the submillimeter images. Thus, at high resolution and sensitivity the far- and mid-IR structure of Vega's disk is predicted to include spiral structure emanating from the submillimeter clumps.
Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.

Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad. fr.
SNPs and interaction analyses of noelin 2, myocilin, and optineurin genes in Japanese patients with open-angle glaucoma.

PURPOSE To evaluate the noelin 2 gene as a disease-causing factor for open-angle glaucoma (OAG) and the interactions between the noelin 2 (OLFM2), optineurin (OPTN), and myocilin (MYOC) genes. METHODS OLFM2 was analyzed in 770 Japanese subjects including 215 patients with elevated intraocular pressure (IOP), 277 with normal IOP, 38 with juvenile open-angle glaucoma, and 240 control subjects. Two single-nucleotide polymorphisms (SNPs) in OPTN (c.412G-->A and c.603T-->A) and one SNP in MYOC (c.227G-->A) were examined. Single genes were investigated by univariate analysis and the gene-gene interactions by logistic regression analysis. Associations between genotypes and clinical characteristics at the time of diagnosis were examined. RESULTS In OLFM2, 12 sequence variants were identified in 770 Japanese subjects. Arg144Gln (exon 4) was identified in two (0.3%) of the patients and in none of the control subjects. Combinations of OLFM2/317A and OPTN/412A or OLFM2/1281T and OPTN/412A were associated with patients with elevated IOP (P = 0.018 or P = 0.012, respectively). The combination of OLFM2/317G and OPTN/603A was significantly associated with elevated IOP (P = 0.018). No significant association was detected between SNPs in OLFM2 and in MYOC. Patients with normal IOP and with OLFM2/678A+OPTN/412G or OLFM2/1281C+OPTN/412G had significantly worse visual field scores (P = 0.022 or 0.030, respectively). CONCLUSIONS The Arg144Gln mutation in OLFM2 is a possible disease-causing mutation in Japanese patients with OAG. Common polymorphisms in OLFM2 and OPTN may interactively contribute to the development of OAG, indicating a polygenic etiology.
Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome.

Properly estimating genetic diversity in populations of nonmodel species requires a basic understanding of how diversity is distributed across the genome and among individuals. To this end, we analysed whole-genome resequencing data from 20 collared flycatchers (genome size ≈1.1 Gb; 10.13 million single nucleotide polymorphisms detected). Genomewide nucleotide diversity was almost identical among individuals (mean = 0.00394, range = 0.00384-0.00401), but diversity levels varied extensively across the genome (95% confidence interval for 200-kb windows = 0.0013-0.0053). Diversity was related to selective constraint such that in comparison with intergenic DNA, diversity at fourfold degenerate sites was reduced to 85%, 3' UTRs to 82%, 5' UTRs to 70% and nondegenerate sites to 12%. There was a strong positive correlation between diversity and chromosome size, probably driven by a higher density of targets for selection on smaller chromosomes increasing the diversity-reducing effect of linked selection. Simulations exploring the ability of sequence data from a small number of genetic markers to capture the observed diversity clearly demonstrated that diversity estimation from finite sampling of such data is bound to be associated with large confidence intervals. Nevertheless, we show that precision in diversity estimation in large outbred population benefits from increasing the number of loci rather than the number of individuals. Simulations mimicking RAD sequencing showed that this approach gives accurate estimates of genomewide diversity. Based on the patterns of observed diversity and the performed simulations, we provide broad recommendations for how genetic diversity should be estimated in natural populations.