Miracle-dz/UniFAR-FTUs huggingface dataset:
NPY Neuron-Specific Y2 Receptors Regulate Adipose Tissue and Trabecular Bone but Not Cortical Bone Homeostasis in Mice

Background Y2 receptor signalling is known to be important in neuropeptide Y (NPY)-mediated effects on energy homeostasis and bone physiology. Y2 receptors are located post-synaptically as well as acting as auto receptors on NPY-expressing neurons, and the different roles of these two populations of Y2 receptors in the regulation of energy homeostasis and body composition are unclear. Methodology/Principal Findings We thus generated two conditional knockout mouse models, Y2lox/lox and NPYCre/+;Y2lox/lox, in which Y2 receptors can be selectively ablated either in the hypothalamus or specifically in hypothalamic NPY-producing neurons of adult mice. Specific deletion of hypothalamic Y2 receptors increases food intake and body weight compared to controls. Importantly, specific ablation of hypothalamic Y2 receptors on NPY-containing neurons results in a significantly greater adiposity in female but not male mice, accompanied by increased hepatic triglyceride levels, decreased expression of liver cartinine palmitoyltransferase (CPT1) and increased expression of muscle phosphorylated acetyl-CoA carboxylase (ACC). While food intake, body weight, femur length, bone mineral content, density and cortical bone volume and thickness are not significantly altered, trabecular bone volume and number were significantly increased by hypothalamic Y2 deletion on NPY-expressing neurons. Interestingly, in situ hybridisation reveals increased NPY and decreased proopiomelanocortin (POMC) mRNA expression in the arcuate nucleus of mice with hypothalamus-specific deletion of Y2 receptors in NPY neurons, consistent with a negative feedback mechanism between NPY expression and Y2 receptors on NPY-ergic neurons. Conclusions/Significance Taken together these data demonstrate the anti-obesogenic role of Y2 receptors in the brain, notably on NPY-ergic neurons, possibly via inhibition of NPY neurons and concomitant stimulation of POMC-expressing neurons in the arcuate nucleus of the hypothalamus, reducing lipogenic pathways in liver and/or skeletal muscle in females. These data also reveal as an anti-osteogenic effect of Y2 receptors on hypothalamic NPY-expressing neurons on trabecular but not on cortical bone.
Dynamic Time & Date Stamp Analysis

• The MAC times of the files involved in the intrusion indicated that SUBJECT intruded on VICTIM systems on December 5, 1998, 1:00am (CST.) • Analysis of the registry indicated the system time zone was set to Pacific Standard Time. • Analysis of the Internet History file corroborated the MAC times by indicating that the intrusion occurred on December 4, 1998, 11:00pm (PST) or December 5, 1998, 1:00am (CST.)
The effect of race/ethnicity on prostate cancer treatment outcome is conditional: a review of Wayne State University data.

PURPOSE The mortality rate for prostate cancer in black American men (AAMs) is 2 times greater than that in other ethnic groups. However, there is considerable controversy as to whether race/ethnicity is an independent predictor of survival outcome. We present conditions in which race/ethnicity is and is not an independent predictor of survival outcomes. MATERIALS AND METHODS We examined the conditions of age, stage and year of diagnosis, and the role of race/ethnicity on disease-free survival in men who underwent consecutive radical prostatectomy as monotherapy from 1990 to 1999. Data were collected from 229 AAMs and 562 white American men prospectively in the Karmanos Cancer Institute Prostate cancer data bases. RESULTS When the majority of the cohort had pathologically organ confined disease, race/ethnicity was not an independent predictor of disease-free survival. When the majority of the cohort had a mean age of 70 years or greater, race/ethnicity was not an independent predictor. In studies done in the late 1990s, when the stage of radical prostatectomy cases had shifted toward pathologically organ confined disease as the dominant stage, race/ethnicity was not an independent predictor. However, if the cohort was diagnosed at younger age and/or with more advanced prostate cancer, race/ethnicity became an independent predictor. In the early 1990s there was pathologically advanced disease in the majority of our cohort. CONCLUSIONS Race/ethnicity as an independent predictor of prostate cancer is conditional and dependent on age, stage and year of diagnosis. Year of diagnosis is associated with a stage shift to earlier staged prostate cancer from the early to late 1990s. In general, study cohorts are often subranges of the entire spectrum of prostate cancer that are limited by these factors, especially stage at diagnosis and treatment. If diagnosed and treated early enough, although there is evidence suggesting that AAMs have more aggressive disease biologically, the role of race as a factor in outcome is significantly decreased. The age factor is more complex and must be discussed in more detail.
Multi-robot coverage on dendritic topologies under communication constraints

This paper proposes a novel algorithm for performing multi-robot coverage on networks with dendritic topology where the communication topology is location dependent and where the motion of each robot is constrained by the presence of the other robots in the network. The algorithm provides complete network coverage by the minimum number of robots, maintenance of communication constraints and robot collision avoidance. The minimum number of robots required for coverage is a by-product of the proposed algorithm. The efficiency of the algorithm is demonstrated through simulation studies.
Histological Observation of Islet Hemorrhage Induced by Diagnostic Ultrasound with Contrast Agent in Rat Pancreas

Contrast enhanced diagnostic ultrasound CEDUS has been shown to induce capillary hemorrhage in heart and kidney. This study characterized the capillary hemorrhage induced in rat pancreas. The pancreata of anesthetized hairless rats were accessed by laparotomy. A 1.5 MHz diagnostic ultrasound probe with 2.3 MPa peak rarefactional pressure amplitude and 1 s intermittent trigger was used to scan the pancreas, located at the focus (3.8 cm), through saline coupling. The probe was swept to expose the entire organ in 5 min during infusion of Definity® contrast agent at 10 µL/kg/min, and this was repeated in a reverse sweep. The entire pancreas was removed, spread flat for fixation and histological slides were prepared from the mid-plane. Slides were scored blind for islet hemorrhage over the entire area of the organ. Intra-islet microlesions were evident and hemorrhage surrounded many islets. The hemorrhage often impacted nearby acini, and expanded into inter-lobular septa. In CEDUS pancreata removed soon after scanning, 76.2±11.8% (n = 6) of islets had evidence of hemorrhage and/or islet microlesions compared to 1.1±2.5% (n = 5) for sham CEDUS (P<0.001). In pancreata removed after 4 hr, fibrin formation was detected by immunohistology in the hemorrhage and intra-islet microlesions. Diagnostic ultrasound with contrast agent induced substantial capillary hemorrhage in rat pancreas, concentrated particularly in the islets.
Driver hand activity analysis in naturalistic driving studies: challenges, algorithms, and experimental studies

Abstract. We focus on vision-based hand activity analysis in the vehicular domain. The study is motivated by the overarching goal of understanding driver behavior, in particular as it relates to attentiveness and risk. First, the unique advantages and challenges for a nonintrusive, vision-based solution are reviewed. Next, two approaches for hand activity analysis, one relying on static (appearance only) cues and another on dynamic (motion) cues, are compared. The motion-cue-based hand detection uses temporally accumulated edges in order to maintain the most reliable and relevant motion information. The accumulated image is fitted with ellipses in order to produce the location of the hands. The method is used to identify three hand activity classes: (1) two hands on the wheel, (2) hand on the instrument panel, (3) hand on the gear shift. The static-cue-based method extracts features in each frame in order to learn a hand presence model for each of the three regions. A second-stage classifier (linear support vector machine) produces the final activity classification. Experimental evaluation with different users and environmental variations under real-world driving shows the promise of applying the proposed systems for both postanalysis of captured driving data as well as for real-time driver assistance.
Spectral Learning of Refinement HMMs

We derive a spectral algorithm for learning the parameters of a refinement HMM. This method is simple, efficient, and can be applied to a wide range of supervised sequence labeling tasks. Like other spectral methods, it avoids the problem of local optima and provides a consistent estimate of the parameters. Our experiments on a phoneme recognition task show that when equipped with informative feature functions, it performs significantly better than a supervised HMM and competitively with EM.
Calibration of cross-sectional images measured by an ultrasound-based muscle evaluation system

The quantification of muscle volume can be used to estimate muscular strength. Therefore, we developed a flexible measuring system for muscle volume using ultrasonog-raphy. In the measuring process, subjects are not required to perform any muscular contraction, so it is completely safe and particularly suitable for elderly people. The ultrasound probe is installed on a mechanical arm, and continuously scans fragmental images along the body surface. The measured images are then composed into a wide area cross-sectional image. However, the muscle area measured by our system was slightly smaller than that measured by MRI. because the ultrasound probe contacted the body surface with a little pressure during the measurement. The strain then decreases the total image size and its circumference. This paper introduces our developed system and proposes a new calibration method for the muscle area in the thigh based on its circumference.
Development, chromosomal composition, and cell allocation of bovine cloned blastocyst derived from chemically assisted enucleation and cultured in conditioned media

Treatment of in vitro matured bovine oocytes with colcemid results in a membrane protrusion that contains maternal chromosomes, which can be easily removed by aspiration. Four experiments were designed to evaluate the overall and temporal effects of conditioned medium (CM) by bovine cumulus cells on development of nuclear transfer (NT) bovine embryos and to examine the chromosomal composition and allocation of inner cell mass (ICM) and trophectoderm (TE) of the subsequent blastocysts. The nuclear transfer embryos were cultured in various CR1aa media conditioned by preculture with bovine cumulus cells. Development to the blastocyst stage in BSA‐containing CM (BCM) and serum‐containing CM (SCM) were similar to co‐culture group (24–30%). The 24 hr‐conditioned BCM yielded higher blastocyst development than 48 and 72 hr‐conditioned BCM. Temporary exposure of embryos to BCM and SCM followed by CR1aa was also studied. Morula and blastocyst development were not different among the groups cultured in BCM for 72, 96, and 168 hr, but were significantly higher (P < 0.01) than groups exposed to BCM for 24 and 48 hr, respectively. Blastocyst development in SCM for 24 hr (29%), 96 hr (25%), and 168 hr (27%) were much higher (P < 0.05) than those in SCM for 48 hr (12%) and 72 hr (10%). The analyses of chromosomal composition of the resulting blastocysts indicate approximately 80% of the blastocysts cultured in CR1aa with co‐culture or groups initially exposed to BCM for 24 hr followed by culture in CR1aa were diploid. However, the incidence of diploidy were only 36–60% in SCM‐cultured groups and groups cultured in BCM beyond 48 hr. Conditioned media did not affect the allocation of ICM and TE in the blastocyst. No difference was found in the ratio of inner cell mass to total cells in co‐culture, BCM or SCM groups (0.424, 0.441, and 0.473, respectively). In conclusion, bovine cumulus cell‐CM and CR1aa with co‐culture supported comparable development and blastocyst ICM:total cell ratio of bovine NT embryos. However, CM affected the blastocyst chromosomal composition and induced higher mixploidy. Mol. Reprod. Dev. 68: 189–197, 2004. © 2004 Wiley‐Liss, Inc.
A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases

Genome‐wide analysis of chitinase genes in the Hypocrea jecorina (anamorph: Trichoderma reesei) genome database revealed the presence of 18 ORFs encoding putative chitinases, all of them belonging to glycoside hydrolase family 18. Eleven of these encode yet undescribed chitinases. A systematic nomenclature for the H. jecorina chitinases is proposed, which designates the chitinases corresponding to their glycoside hydrolase family and numbers the isoenzymes according to their pI from Chi18‐1 to Chi18‐18. Phylogenetic analysis of H. jecorina chitinases, and those from other filamentous fungi, including hypothetical proteins of annotated fungal genome databases, showed that the fungal chitinases can be divided into three groups: groups A and B (corresponding to class V and III chitinases, respectively) also contained the so Trichoderma chitinases identified to date, whereas a novel group C comprises high molecular weight chitinases that have a domain structure similar to Kluyveromyces lactis killer toxins. Five chitinase genes, representing members of groups A–C, were cloned from the mycoparasitic species H. atroviridis (anamorph: T. atroviride). Transcription of chi18‐10 (belonging to group C) and chi18‐13 (belonging to a novel clade in group B) was triggered upon growth on Rhizoctonia solani cell walls, and during plate confrontation tests with the plant pathogen R. solani. Therefore, group C and the novel clade in group B may contain chitinases of potential relevance for the biocontrol properties of Trichoderma.
Dermal fibroblasts respond to mechanical conditioning in a strain profile dependent manner.

Fibroblasts within tissues are exposed to a dynamic mechanical environment, which influences the structural integrity of both healthy and healing soft tissues. Various systems have been proposed to subject such cells to mechanical stimulation in culture. However the diverse nature of the studies, in terms of the strain profiles and the cell types, makes direct comparisons almost impossible. The present study addresses this issue by examining the metabolic response of two cell types subjected to three well defined strain profiles.A young fibroblast cell population, represented by HuFFs, showed both greater cell proliferation and collagen production than adult dermal fibroblasts under unstrained conditions. The three strain profiles produced differing effects on both cell types. Uniaxial strains enhanced [(3)H]-thymidine incorporation for both cell types, whilst biaxial strains either inhibited or had no effect on its incorporation. In contrast, [(3)H]-proline incorporation was inhibited under biaxial and uniaxial strains for the adult fibroblasts, whilst the HuFF cells showed a small increase in proline incorporation under non-uniform and uniaxial strains.
On the Role of the Ventromedial Prefrontal Cortex in Self-Processing: The Valuation Hypothesis

With the development of functional neuroimaging, important progress has been made in identifying the brain regions involved in self-related processing. One of the most consistent findings has been that the ventromedial prefrontal cortex (vMPFC) is activated when people contemplate various aspects of themselves and their life, such their traits, experiences, preferences, abilities, and goals. Recent evidence suggests that this region may not support the act of self-reflection per se, but its precise function in self-processing remains unclear. In this article, I examine the hypothesis that the vMPFC may contribute to assign personal value or significance to self-related contents: stimuli and mental representations that refer or relate to the self tend to be assigned unique value or significance, and the function of the vMPFC may precisely be to evaluate or represent such significance. Although relatively few studies to date have directly tested this hypothesis, several lines of evidence converge to suggest that vMPFC activity during self-processing depends on the personal significance of self-related contents. First, increasing psychological distance from self-representations leads to decreased activation in the vMPFC. Second, the magnitude of vMPFC activation increases linearly with the personal importance attributed to self-representations. Third, the activity of the vMPFC is modulated by individual differences in the interest placed on self-reflection. Finally, the evidence shows that the vMPFC responds to outer aspects of self that have high personal value, such as possessions and close others. By assigning personal value to self-related contents, the vMPFC may play an important role in the construction, stabilization, and modification of self-representations, and ultimately in guiding our choices and decisions.
Interdisciplinary approaches to understanding disease emergence: The past, present, and future drivers of Nipah virus emergence

Emerging infectious diseases (EIDs) pose a significant threat to human health, economic stability, and biodiversity. Despite this, the mechanisms underlying disease emergence are still not fully understood, and control measures rely heavily on mitigating the impact of EIDs after they have emerged. Here, we highlight the emergence of a zoonotic Henipavirus, Nipah virus, to demonstrate the interdisciplinary and macroecological approaches necessary to understand EID emergence. Previous work suggests that Nipah virus emerged due to the interaction of the wildlife reservoir (Pteropus spp. fruit bats) with intensively managed livestock. The emergence of this and other henipaviruses involves interactions among a suite of anthropogenic environmental changes, socioeconomic factors, and changes in demography that overlay and interact with the distribution of these pathogens in their wildlife reservoirs. Here, we demonstrate how ecological niche modeling may be used to investigate the potential role of a changing climate on the future risk for Henipavirus emergence. We show that the distribution of Henipavirus reservoirs, and therefore henipaviruses, will likely change under climate change scenarios, a fundamental precondition for disease emergence in humans. We assess the variation among climate models to estimate where Henipavirus host distribution is most likely to expand, contract, or remain stable, presenting new risks for human health. We conclude that there is substantial potential to use this modeling framework to explore the distribution of wildlife hosts under a changing climate. These approaches may directly inform current and future management and surveillance strategies aiming to improve pathogen detection and, ultimately, reduce emergence risk.
A Comparison of Quantitative Ultrasound of the Calcaneus With Dual-Energy X-ray Absorptiometry in Hospitalized Orthopaedic Trauma Patients

Objectives: Osteoporosis remains underdiagnosed in orthopaedic trauma patients. Recently, protocols have emerged to identify and treat osteoporosis in this population. Our purpose was to compare the usefulness of quantitative ultrasound of calcaneus (QUS) with dual-energy x-ray absorptiometry (DXA) for identifying orthopaedic trauma patients at risk for osteoporotic fractures. Design: A retrospective review of an osteoporosis screening protocol comparing QUS and DXA. Setting: Regional trauma center. Patients: Three hundred sixty consecutive hospitalized orthopaedic trauma patients treated by a single surgeon. Intervention: QUS T-score and DXA bone mineral density T-scores (hip or radius) were obtained relative to U.S. normative data. Main Outcome Measurements: QUS and DXA data were statistically compared to analyze their relationship. Potential thresholds for osteoporosis risk were subsequently defined. Results: Testing was successfully performed with heel QUS in 350 patients and with DXA in 129 patients. One hundred twenty-six patients underwent testing with both modalities. According to World Health Organization criteria, 17% of patients tested with DXA had osteoporosis. A good predictive relationship between hip bone mineral density, as estimated by calcaneal QUS, and direct DXA measurement was seen (Pearson's r correlation coefficient of 0.53; area under the curve of 0.84 with 95% confidence interval = 0.75-0.90; P = 0.0001). QUS T-score cutoffs of greater than −0.9 resulted in 90% sensitivity (defining low osteoporosis risk) and a threshold of −1.6 or less resulted in a specificity of 80% (defining high osteoporosis risk). Conclusions: Substantial logistical difficulties are inherent in attempting to obtain DXA scans in orthopaedic trauma patients at our regional trauma center. For those patients who did undergo DXA, a strong predictive relationship was seen between hip bone mineral density and QUS parameters. QUS thresholds in defining low- and high-risk subjects for osteoporosis in this population using this device are proposed. QUS is a simple, reliable, and relatively inexpensive tool for evaluating osteoporosis risk in orthopaedic trauma patients.
Opening the Black Box: Low-Dimensional Dynamics in High-Dimensional Recurrent Neural Networks

Recurrent neural networks (RNNs) are useful tools for learning nonlinear relationships between time-varying inputs and outputs with complex temporal dependencies. Recently developed algorithms have been successful at training RNNs to perform a wide variety of tasks, but the resulting networks have been treated as black boxes: their mechanism of operation remains unknown. Here we explore the hypothesis that fixed points, both stable and unstable, and the linearized dynamics around them, can reveal crucial aspects of how RNNs implement their computations. Further, we explore the utility of linearization in areas of phase space that are not true fixed points but merely points of very slow movement. We present a simple optimization technique that is applied to trained RNNs to find the fixed and slow points of their dynamics. Linearization around these slow regions can be used to explore, or reverse-engineer, the behavior of the RNN. We describe the technique, illustrate it using simple examples, and finally showcase it on three high-dimensional RNN examples: a 3-bit flip-flop device, an input-dependent sine wave generator, and a two-point moving average. In all cases, the mechanisms of trained networks could be inferred from the sets of fixed and slow points and the linearized dynamics around them.
A comparison between LQR control for a long string of 2 × 2 MIMO systems and LQR control of the infinite spatially invariant version

We compare the LQR control for a long-but-finite string of 2 × 2 MIMO systems with the LQR control for the corresponding infinite-dimensional spatially invariant system. We provide analytical and numerical examples where these are different and we investigate the cause. We also provide sufficient conditions for the LQR solutions to be similar as the length of the string increases. This work extends to the 2 × 2 MIMO systems part of the analysis presented in recent papers for the scalar case.