Miracle-dz/UniFAR-FTUs huggingface dataset:
Drosophila PEBP1 inhibits intestinal stem cell aging via suppression of ERK pathway

The intestine is a high cellular turnover tissue largely dependent on the regenerative function of stem cell throughout life, and a signaling center for the health and viability of organisms. Therefore, better understanding of the mechanisms underlying the regulation of intestinal stem cell (ISC) regenerative potential is essential for the possible intervention of aging process and age-related diseases. Drosophila midgut is a well-established model system for studying the mechanisms underlying ISC regenerative potential during aging. Here, we report the requirement of Drosophila phosphatidylethanolamine binding protein 1 (PEBP1) in ISC regenerative potential. We showed that PEBP1 was strongly expressed in enterocytes (ECs) of guts and its decrease with age and oxidative stress. Furthermore, the downregulation of PEBP1 in ECs accelerates ISC aging, as evidenced by ISC hyper-proliferation, γH2AX accumulation, and centrosome amplification, and intestinal hyperplasia. The decrease in PEBP1 expression was associated with increased extracellular signal-regulated kinase (ERK) activity in ECs. All these phenotypes by EC-specific depletion of PEBP1 were rescued by the concomitant inhibition of ERK signaling. Our findings evidence that the age-related downregulation of PEBP1 in ECs is a novel cause accelerating ISC aging and that PEBP1 is an EC-intrinsic suppressor of epidermal growth factor receptor (EGFR)/ERK signaling. Our study provides molecular insights into the tight regulation of EGFR/ERK signaling in niches for stem cell regenerative potential.
Genome-Wide Transcriptional Profiling of Skin and Dorsal Root Ganglia after Ultraviolet-B-Induced Inflammation

Ultraviolet-B (UVB)-induced inflammation produces a dose-dependent mechanical and thermal hyperalgesia in both humans and rats, most likely via inflammatory mediators acting at the site of injury. Previous work has shown that the gene expression of cytokines and chemokines is positively correlated between species and that these factors can contribute to UVB-induced pain. In order to investigate other potential pain mediators in this model we used RNA-seq to perform genome-wide transcriptional profiling in both human and rat skin at the peak of hyperalgesia. In addition we have also measured transcriptional changes in the L4 and L5 DRG of the rat model. Our data show that UVB irradiation produces a large number of transcriptional changes in the skin: 2186 and 3888 genes are significantly dysregulated in human and rat skin, respectively. The most highly up-regulated genes in human skin feature those encoding cytokines (IL6 and IL24), chemokines (CCL3, CCL20, CXCL1, CXCL2, CXCL3 and CXCL5), the prostanoid synthesising enzyme COX-2 and members of the keratin gene family. Overall there was a strong positive and significant correlation in gene expression between the human and rat (R = 0.8022). In contrast to the skin, only 39 genes were significantly dysregulated in the rat L4 and L5 DRGs, the majority of which had small fold change values. Amongst the most up-regulated genes in DRG were REG3B, CCL2 and VGF. Overall, our data shows that numerous genes were up-regulated in UVB irradiated skin at the peak of hyperalgesia in both human and rats. Many of the top up-regulated genes were cytokines and chemokines, highlighting again their potential as pain mediators. However many other genes were also up-regulated and might play a role in UVB-induced hyperalgesia. In addition, the strong gene expression correlation between species re-emphasises the value of the UVB model as translational tool to study inflammatory pain.
Concurrent transmission versus time sharing in Gaussian interference channels

A key to efficient mobile communication networks is an efficient utilization of scarce resources, which includes mechanisms for resource allocation and interference management. In practice, time sharing methods such as Time Division Multiple Access (TDMA) are often exploited to create orthogonal connections. TDMA schemes however are inflexible and not suitable for decentralized implementation. In this context, approaches based on concurrent transmissions in the same frequency spectrum admitting the interference offer a promising and attractive alternative. Yet their performances deteriorate dramatically if the underlying interference coefficients are relatively large. Assuming a Gaussian Interference Channel (GIC), this paper characterizes the so-called TDMA region which is defined as a set of all interference coefficient matrices for which TDMA outperforms concurrent transmissions. We use the dimensional lifting method to prove the convexity and monotonicity of the TDMA region, which provides some insights into the scheduling design under uncertainty with respect to the interference coefficients. Finally, the analysis is used to develop strategies for resource allocation in STDMA-based wireless networks.
A Comparison between Clinical Results of Selective Bundle and Double Bundle Anterior Cruciate Ligament Reconstruction

Purpose The purpose of this study was to compare the clinical outcomes of arthroscopic anatomical double bundle (DB) anterior cruciate ligament (ACL) reconstruction with either selective anteromedial (AM) or posterolateral (PL) bundle reconstruction while preserving a relatively healthy ACL bundle. Materials and Methods The authors evaluated 98 patients with a mean follow-up of 30.8±4.0 months who had undergone DB or selective bundle ACL reconstructions. Of these, 34 cases underwent DB ACL reconstruction (group A), 34 underwent selective AM bundle reconstruction (group B), and 30 underwent selective PL bundle reconstructions (group C). These groups were compared with respect to Lysholm and International Knee Documentation Committee (IKDC) score, side-to-side differences of anterior laxity measured by KT-2000 arthrometer at 30 lbs, and stress radiography and Lachman and pivot shift test results. Pre- and post-operative data were objectively evaluated using a statistical approach. Results The preoperative anterior instability measured by manual stress radiography at 90° of knee flexion in group A was significantly greater than that in groups B and C (all p<0.001). At last follow-up, mean side-to-side instrumented laxities measured by the KT-2000 and manual stress radiography were significantly improved from preoperative data in all groups (all p<0.001). There were no significant differences between the three groups in anterior instability measured by KT-2000 arthrometer, pivot shift, or functional scores. Conclusion Selective bundle reconstruction in partial ACL tears offers comparable clinical results to DB reconstruction in complete ACL tears.
Representation of Objects and Events : Why Do Infants Look So Smart and Toddlers Look So Dumb ?

Theories of attention, too often generated from artificial laboratory experiments, may have limited validity when attention in the natural world is considered. For instance, for more than two decades, conceptualiza-tions of " reflexive " and " voli-tional " shifts of spatial attention have been grounded in method-ologies that do not recognize or utilize the basic fact that people routinely use the eyes of other people as rich and complex at-tentional cues. This fact was confirmed by our novel discovery that eyes will trigger a reflexive shift of attention even when they are presented centrally and are known to be spatially nonpre-dictive. This exploration of real-world attention also led to our finding that, contrary to popular wisdom, arrows, like eyes, are capable of producing reflexive shifts of attention—a discovery that brings into question much of the existing attention research. We argue that research needs to be grounded in the real world and not in experimental paradigms. It is time for cogni-tive psychology to reaffirm the difficult task of studying attention in a manner that has relevance to real-life situations. The researcher remote from immediate practical pressures may indeed be free to study major variables in which at this instant society does not seem to be interested; but he should not use this freedom in order to study minor variables, until there are no major ones within reach of our techniques. The necessity for some relevance to real life is a worthwhile intellectual discipline. Broadbent is one of the most significant researchers in experimental psychology. His research and writings on attention helped to initiate and fuel the paradigm shift known as the cognitive revolution. Broadbent was adamant that psychological theory must be grounded in real-life experiences. We argue, in part on the basis of recent findings from our lab, that cognitive psychology has, over time, lost touch with this foundation. The result is that theories of attention, often arising out of artificial laboratory experiments, fail to generalize to the real world. Thus, researchers are often unable to ask, let alone answer, many major questions regarding the everyday functioning of attention. methodology that would come to be known as the Posner cuing paradigm was introduced. Since then, it has been used routinely to study human spatial attention. In this paradigm, a central fixation dot is flanked by two squares (boxes). The task is to make a key press as quickly as possible when …
Internalization of Salmonella by Macrophages Induces Formation of Nonreplicating Persisters

Persistent Survival The role of persister cells—dormant cells that survive multidrug treatment—in the context of bacterial pathogenesis has not been explored in depth. Using a single-cell fluorescent dilution technique, Helaine et al. (p. 204) examined Salmonella Typhimurium persister-cell formation in vitro and in infections in mice. Within 30 min after phagocytosis by macrophages, Salmonella cells follow one of two fates, either to replication and generation of virulence effectors or to remaining viable but become nonreplicating persisters. Salmonella living within a macrophage vacuole are exposed to potentially stressful conditions that induce the expression of 14 Type II toxin-antidote loci in a ppGpp/lon protease-dependent manner, and this system appears to play a role in both virulence factor induction and persister-cell formation. The nonreplicating bacteria represent at least four distinct subpopulations, as defined by their ability to resume growth and their metabolic activity, but different phenotypes are observed in different pathogens and Escherichia coli persisters are distinct from Salmonella persisters. Upon internalization, intracellular Salmonella choose between replication or a form of quiescence known as persistence. Many bacterial pathogens cause persistent infections despite repeated antibiotic exposure. Bacterial persisters are antibiotic-tolerant cells, but little is known about their growth status and the signals and pathways leading to their formation in infected tissues. We used fluorescent single-cell analysis to identify Salmonella persisters during infection. These were part of a nonreplicating population formed immediately after uptake by macrophages and were induced by vacuolar acidification and nutritional deprivation, conditions that also induce Salmonella virulence gene expression. The majority of 14 toxin-antitoxin modules contributed to intracellular persister formation. Some persisters resumed intracellular growth after phagocytosis by naïve macrophages. Thus, the vacuolar environment induces phenotypic heterogeneity, leading to either bacterial replication or the formation of nonreplicating persisters that could provide a reservoir for relapsing infection.
Evaluation of the DSM‐5 Severity Indicator for Anorexia Nervosa

OBJECTIVE This study tested the new DSM-5 severity criterion for anorexia nervosa (AN) based on proposed body mass index (BMI) cut-points. METHOD Participants were a clinical sample of 201 treatment-seeking patients diagnosed with DSM-5 AN in Portugal. Participants were categorised based on DSM-5 severity levels and were compared on demographic and clinical variables assessed with the Eating Disorder Examination-Questionnaire. RESULTS Based on DSM-5 severity definitions for AN, 73 (36.3%) participants were categorised as mild (≥17.0 BMI), 40 (19.9%) as moderate (16-16.99 BMI), 30 (14.9%) as severe (15-15.99 BMI) and 58 (28.9%) as extreme (<15 BMI). The severity groups did not differ significantly in age or gender. Analyses comparing the severity groups on measures of eating-disorder psychopathology revealed no significant differences on the Eating Disorder Examination-Questionnaire global or subscale scores. The groups also did not differ significantly on the frequency of binge eating or purging episodes within the past 28 days. CONCLUSIONS Our findings, in this clinical sample of patients with AN in Portugal, provide no evidence for the new DSM-5 severity ratings based on BMI level. Further research on the validity of the DSM-5 specifiers is needed and should test additional clinical or functional variables and especially prognostic utility for course and outcome across eating disorders. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association.
Staging RANSAC: An indoor camera calibration method

This paper proposes a method of extrinsically calibrating cameras in a rectangular room-like environment. It searches for line segments to indicate planar surfaces in the scene, mainly floor, walls and ceiling and uses the homographical relation between matching features on those surfaces to solve for the calibration parameters of the camera and the planes. It is assumed that the environment follows the Manhattan-assumption, i.e. has orthogonal main directions, but we also propose solutions for the general case. We argue that this approach, together with its ability to help describing affine-invariant features to find a larger amount of correct matches, contributes to a larger robustness over epipolar constraint based methods. Due to its cascade-like nature, the method will yield a less accurate estimate, though it serves well as a starting point for bundle adjustment.
Early T-Cell Responses to Dengue Virus Epitopes in Vietnamese Adults with Secondary Dengue Virus Infections

ABSTRACT T-cell responses to dengue viruses may be important in both protective immunity and pathogenesis. This study of 48 Vietnamese adults with secondary dengue virus infections defined the breadth and magnitude of peripheral T-cell responses to 260 overlapping peptide antigens derived from a dengue virus serotype 2 (DV2) isolate. Forty-seven different peptides evoked significant gamma interferon enzyme-linked immunospot (ELISPOT) assay responses in 39 patients; of these, 34 peptides contained potentially novel T-cell epitopes. NS3 and particularly NS3200-324 were important T-cell targets. The breadth and magnitude of ELISPOT responses to DV2 peptides were independent of the infecting dengue virus serotype, suggesting that cross-reactive T cells dominate the acute response during secondary infection. Acute ELISPOT responses were weakly correlated with the extent of hemoconcentration in individual patients but not with the nadir of thrombocytopenia or overall clinical disease grade. NS3556-564 and Env414-422 were identified as novel HLA-A*24 and B*07-restricted CD8+ T-cell epitopes, respectively. Acute T-cell responses to natural variants of Env414-422 and NS3556-564 were largely cross-reactive and peaked during disease convalescence. The results highlight the importance of NS3 and cross-reactive T cells during acute secondary infection but suggest that the overall breadth and magnitude of the T-cell response is not significantly related to clinical disease grade.
Why Retailers Sell More or Less Than Their Fair Share in a Category

Assessing a retailer’s performance in a category is important to both manufacturers and retailers. The main objective of this paper is to understand the factors that determine across-retailer variation in category performance as measured by the Category Development Index (CDI). Based on data from 19 food categories sold in 85 major supermarket chains operating in the largest 50 retail markets in the U.S, our analysis shows that the best performing retailers: (a) offer broader assortments, (b) have strong private label programs, (c) charge significantly lower everyday prices, and (d) use feature advertising to drive store traffic and display to increase in-store purchases. In addition, the best performing retailers also are more likely to engage in a formal category management process. Finally, we find that the impact of the price, promotion and assortment variables depends importantly on the role (staple, variety enhancers, niche, or fill-in) that the particular category plays in the store’s overall portfolio.
Stereological methods reveal the robust size and stability of ectopic hilar granule cells after pilocarpine‐induced status epilepticus in the adult rat

Following status epilepticus in the rat, dentate granule cell neurogenesis increases greatly, and many of the new neurons appear to develop ectopically, in the hilar region of the hippocampal formation. It has been suggested that the ectopic hilar granule cells could contribute to the spontaneous seizures that ultimately develop after status epilepticus. However, the population has never been quantified, so it is unclear whether it is substantial enough to have a strong influence on epileptogenesis. To quantify this population, the total number of ectopic hilar granule cells was estimated using unbiased stereology at different times after pilocarpine‐induced status epilepticus. The number of hilar neurons immunoreactive for Prox‐1, a granule‐cell‐specific marker, was estimated using the optical fractionator method. The results indicate that the size of the hilar ectopic granule cell population after status epilepticus is substantial, and stable over time. Interestingly, the size of the population appears to be correlated with the frequency of behavioral seizures, because animals with more ectopic granule cells in the hilus have more frequent behavioral seizures. The hilar ectopic granule cell population does not appear to vary systematically across the septotemporal axis, although it is associated with an increase in volume of the hilus. The results provide new insight into the potential role of ectopic hilar granule cells in the pilocarpine model of temporal lobe epilepsy.
Progesterone administration does not acutely alter LH pulse secretion in the mid‐follicular phase in women

It remains unclear how rapidly progesterone suppresses luteinizing hormone (LH) pulse frequency in women. Previous studies suggested that progesterone markedly increases LH pulse amplitude but does not slow LH pulse frequency within 10 h in estradiol‐pretreated women studied during the late follicular phase. However, this experimental paradigm may be a model of preovulatory physiology, and progesterone may have different effects at other times of the cycle. We studied regularly cycling, nonobese women without hyperandrogenism to assess the acute effect of progesterone during the midfollicular phase and in the absence of estradiol pretreatment. The study involved two admissions in separate cycles (cycle days 5–9). For each admission, either oral micronized progesterone (100 mg) or placebo was administered at 0900 h in a randomized, double‐blind fashion. Frequent blood sampling was performed between 0900 and 1900 h to define 10‐h LH pulsatility. Treatment crossover (placebo exchanged for progesterone and vice versa) occurred in a subsequent cycle. After an interim futility analysis, the study was halted after 7 women completed study. Mean progesterone concentrations after placebo and progesterone administration were 0.5 ± 0.1 (mean ± SD) and 6.7 ± 1.6 ng/mL, respectively. Compared to placebo, progesterone was not associated with a significant difference in 10‐h LH pulse frequency (0.79 ± 0.35 vs. 0.77 ± 0.28 pulses/h, P = 1.0) or amplitude (3.6 ± 2.8 vs. 4.3 ± 2.8 IU/L, P = 0.30). This study suggests that LH pulse frequency is not rapidly influenced by progesterone administration during the midfollicular phase.
Parasite interactions in natural populations: insights from longitudinal data

SUMMARY The physiological and immunological state of an animal can be influenced by current infections and infection history. Consequently, both ongoing and previous infections can affect host susceptibility to another parasite, the biology of the subsequent infection (e.g. infection length) and the impact of infection on host morbidity (pathology). In natural populations, most animals will be infected by a succession of different parasites throughout the course of their lives, with probably frequent concomitant infections. The relative timing of different infections experienced by a host (i.e. the sequence of infection events), and the effects on factors such as host susceptibility and host survival, can only be derived from longitudinal data on individual hosts. Here we review some of the evidence for the impact of co-infection on host susceptibility, infection biology and pathology focusing on insights obtained from both longitudinal studies in humans and experiments that explicitly consider the sequence of infection. We then consider the challenges posed by longitudinal infection data collected from natural populations of animals. We illustrate their usefulness using our data of microparasite infections associated with field vole (Microtus agrestis) populations to examine impacts on susceptibility and infection length. Our primary aim is to describe an analytical approach that can be used on such data to identify interactions among the parasites. The preliminary analyses presented here indicate both synergistic and antagonistic interactions between microparasites within this community and emphasise that such interactions could have significant impacts on host-parasite fitness and dynamics.
Embedding a Semantic Network in a Word Space

We present a framework for using continuousspace vector representations of word meaning to derive new vectors representing the meaning of senses listed in a semantic network. It is a post-processing approach that can be applied to several types of word vector representations. It uses two ideas: first, that vectors for polysemous words can be decomposed into a convex combination of sense vectors; secondly, that the vector for a sense is kept similar to those of its neighbors in the network. This leads to a constrained optimization problem, and we present an approximation for the case when the distance function is the squared Euclidean. We applied this algorithm on a Swedish semantic network, and we evaluate the quality of the resulting sense representations extrinsically by showing that they give large improvements when used in a classifier that creates lexical units for FrameNet frames.