Miracle-dz/UniFAR-FTUs huggingface dataset:
Using the Single Prolonged Stress Model to Examine the Pathophysiology of PTSD

The endurance of memories of emotionally arousing events serves the adaptive role of minimizing future exposure to danger and reinforcing rewarding behaviors. However, following a traumatic event, a subset of individuals suffers from persistent pathological symptoms such as those seen in posttraumatic stress disorder (PTSD). Despite the availability of pharmacological treatments and evidence-based cognitive behavioral therapy, a considerable number of PTSD patients do not respond to the treatment, or show partial remission and relapse of the symptoms. In controlled laboratory studies, PTSD patients show deficient ability to extinguish conditioned fear. Failure to extinguish learned fear could be responsible for the persistence of PTSD symptoms such as elevated anxiety, arousal, and avoidance. It may also explain the high non-response and dropout rates seen during treatment. Animal models are useful for understanding the pathophysiology of the disorder and the development of new treatments. This review examines studies in a rodent model of PTSD with the goal of identifying behavioral and physiological factors that predispose individuals to PTSD symptoms. Single prolonged stress (SPS) is a frequently used rat model of PTSD that involves exposure to several successive stressors. SPS rats show PTSD-like symptoms, including impaired extinction of conditioned fear. Since its development by the Liberzon lab in 1997, the SPS model has been referred to by more than 200 published papers. Here we consider the findings of these studies and unresolved questions that may be investigated using the model.
Dynamic Jointrees

It is well known that one can ignore parts of a belief network when computing answers to certain probabilistic queries. It is also well known that the ignorable parts (if any) depend on the specific query of interest and, therefore, may change as the query changes. Algorithms based on jointrees, however, do not seem to take computational advantage of these facts given that they typically construct jointrees for worst-case queries; that is, queries for which every part of the belief network is considered relevant. To address this limitation, we propose in this paper a method for reconfiguring jointrees dynamically as the query changes. The reconfiguration process aims at maintaining a jointree which corresponds to the underlying belief network after it has been pruned given the current query. Our reconfiguration method is marked by three characteristics: (a) it is based on a nonclassical definition of jointrees; (b) it is relatively efficient; and (c) it can reuse some of the computations performed before a jointree is reconfigured. We present preliminary experimental results which demonstrate significant savings over using static jointrees when query changes are considerable.
Co-occurring Notonecta (Hemiptera: Heteroptera: Notonectidae) Species Differ in Their Behavioral Response to Cues of Belostoma (Hemiptera: Heteroptera: Belostomatidae) Predation Risk

Abstract Predators affect prey through direct consumption as well as by inducing prey to defensively alter their phenotypes, including behavioral phenotypes, to maximize survival under predation risk. Closely related sympatric prey species with shared natural enemies may resolve behavioral trade-offs under predation risk differently. In a laboratory experiment, we investigated two co-occurring semiaquatic backswimmer congeners, which exhibit differences in their degree of habitat specialization across a gradient of habitat permanence. Notonecta irrorata Uhler primarily occur in ephemeral ponds, whereas Notonecta undulata Say are habitat generalists that are commonly found in both permanent and ephemeral ponds.We tested whether the two species differed in antipredator responses to both visual and chemical cues of a shared predator, the giant water bug, in a fully factorial design.The generalist species, N. undulata, exhibited reductions in activity in the presence of predator chemical cues only, whereas the specialist species, N. irrorata, remained consistently active across predator cue treatments. Our work shows that there are species-specific differences in how prey assess or respond to predation risk.The varying propensities of these backswimmer congeners to behaviorally respond to a shared predator, and differences in their behavior when exposed to different predation risk cues may be linked to underlying divergence in their life-history strategies.
Progress Towards A Permanent Octupole Magnetic Ultra-Cold Neutron Trap for Lifetime Measurements

The current knowledge of the neutron $\beta$-decay lifetime has come under scrutiny as of late due to large disagreements between recent precise measurements. Measurements using magnetically trapped Ultra-Cold Neutrons (UCNs) offer the possibility of storage without spurious losses which can provide a reliable value for the neutron lifetime. The progress towards realizing a neutron lifetime measurement using a Ioffe-type trap made with a Halbach-type permanent octupole magnet is presented here. The experimental procedure extracts a gas of UCNs into vacuum, which reduces many known channels of neutron losses, and detects the neutron decays via in-situ detection of the produced protons.
Neutralization of Interleukin-16 Protects Nonobese Diabetic Mice From Autoimmune Type 1 Diabetes by a CCL4-Dependent Mechanism

OBJECTIVE The progressive infiltration of pancreatic islets by lymphocytes is mandatory for development of autoimmune type 1 diabetes. This inflammatory process is mediated by several mediators that are potential therapeutic targets to arrest development of type 1 diabetes. In this study, we investigate the role of one of these mediators, interleukin-16 (IL-16), in the pathogenesis of type 1 diabetes in NOD mice. RESEARCH DESIGN AND METHODS At different stages of progression of type 1 diabetes, we characterized IL-16 in islets using GEArray technology and immunoblot analysis and also quantitated IL-16 activity in cell migration assays. IL-16 expression was localized in islets by immunofluorescence and confocal imaging. In vivo neutralization studies were performed to assess the role of IL-16 in the pathogenesis of type 1 diabetes. RESULTS The increased expression of IL-16 in islets correlated with the development of invasive insulitis. IL-16 immunoreactivity was found in islet infiltrating T-cells, B-cells, NK-cells, and dendritic cells, and within an insulitic lesion, IL-16 was derived from infiltrating cells. CD4+ and CD8+ T-cells as well as B220+ B-cells were identified as sources of secreted IL-16. Blockade of IL-16 in vivo protected against type 1 diabetes by interfering with recruitment of CD4+ T-cells to the pancreas, and this protection required the activity of the chemokine CCL4. CONCLUSIONS IL-16 production by leukocytes in islets augments the severity of insulitis during the onset of type 1 diabetes. IL-16 and CCL4 appear to function as counterregulatory proteins during disease development. Neutralization of IL-16 may represent a novel therapy for the prevention of type 1 diabetes.
A Learning Based Depth Estimation Framework for 4D Densely and Sparsely Sampled Light Fields

This paper proposes a learning based solution to disparity (depth) estimation for either densely or sparsely sampled light fields. Disparity between stereo pairs among a sparse subset of anchor views is first estimated by a fine-tuned FlowNet 2.0 network adapted to disparity prediction task. These coarse estimates are fused by exploiting the photo-consistency warping error, and refined by a Multi-view Stereo Refinement Network (MSRNet). The propagation of disparity from anchor viewpoints towards other viewpoints is performed by an occlusion-aware soft 3D reconstruction method. The experiments show that, both for dense and sparse light fields, our algorithm outperforms significantly the state-of-the-art algorithms, especially for subpixel accuracy.
Amino Acid Biosynthesis by Isolated Chloroplasts during Photosynthesis.

The pool sizes of the common amino acids in purified intact chloroplasts from Vicia faba L. were measured (nanomoles per milligram chlorophyll). The three amino acids present in the highest concentrations were glutamate, aspartate, and threonine. Alanine, serine, and glycine were each present at levels between 15 and 20 nanomoles per milligram chlorophyll and 13 other amino acids were detectable at levels below 10.Only aspartate, alanine, glycine, serine, threonine, and lysine became labeled during photosynthetic (14)CO(2) fixation by isolated chloroplasts: the label in aspartate represented over 60% of the total (14)C found in the amino acids. Glutamate dehydrogenase, glutamate-oxaloacetate, and glutamate-pyruvate aminotransferases were present in the chloroplasts, but no other transferase activities from glutamate could be detected. The chloroplasts were able to synthesize a total of 17 other protein amino acids from either alanine or aspartate, but no synthesis of leucine by aminotransferase reactions could be detected. The synthesis of aspartate was studied in more detail. The enzyme systems required for the generation of oxaloacetate from triose phosphate were virtually absent from the chloroplasts but present in the leaf cytoplasmic fraction. Addition of either a leaf "cytoplasmic" fraction or an oxaloacetate generating system resulted in an increased proportion of the total (14)C fixed being found in the amino acid fraction during photosynthetic (14)CO(2) fixation.It is suggested that the supply of oxaloacetate from the cytoplasm is one of the important factors controlling the synthesis of amino acids by the chloroplast.
Effect of a Six-week-intervention with an Activity-promoting Video Game on Isometric Muscle Strength in Elderly Subjects

In order to analyze the effect of a six-week intervention with an activity-promoting video game on muscle strength in elderly subjects (> 60 years) a controlled pretest-posttest study was conducted. The intervention group performed a 20-minutes session playing Wii bowling, twice a week for a total of six weeks. Data was analyzed by use of an ANCOVA. When comparing the results with the control group findings, the isometric muscle strength of the m. quadriceps increased significantly. Thus, an activity-promoting video game such as bowling with a Wii leads to functional improvement and might have positive health implications for elderly people.
First evidence of TRPV5 and TRPV6 channels in human parathyroid glands: possible involvement in neoplastic transformation

The parathyroid glands play an overall regulatory role in the systemic calcium (Ca2+) homeostasis. The purpose of the present study was to demonstrate the presence of the Ca2+ channels transient receptor potential vanilloid (TRPV) 5 and TRPV6 in human parathyroid glands. Semi‐quantitative and quantitative PCR was carried out to evaluate the presence of TRPV5 and TRPV6 mRNAs in sporadic parathyroid adenomas and normal parathyroid glands. Western blot and immunocytochemical assays were used to assess protein expression, cellular localization and time expression in primary cultures from human parathyroid adenoma. TRPV5 and TRPV6 transcripts were then identified both in normal and pathological tissues. Predominant immunoreactive bands were detected at 75–80 kD for both vanilloid channels. These channels co‐localized with the calcium‐sensing receptor (CASR) on the membrane surface, but immunoreactivity was also detected in the cytosol and around the nuclei. Our data showed that western blotting recorded an increase of protein expression of both channels in adenoma samples compared with normal glands suggesting a potential relation with the cell calcium signalling pathway and the pathological processes of these glands.
Chained Compressed Sensing for Iot Node Security

Compressed sensing can be used to yield both compression and a limited form of security to the readings of sensors. This can be most useful when designing the low-resources sensor nodes that are the backbone of IoT applications. Here, we propose to use chaining of subsequent plaintexts to improve the robustness of CS-based encryption against ciphertext-only attacks, known-plaintext attacks and man-in-the-middle attacks.
A Constrained Randomization Approach to Interactive Visual Data Exploration with Subjective Feedback

Data visualization and iterative/interactive data mining are growing rapidly in attention, both in research as well as in industry. However, while there are a plethora of advanced data mining methods and lots of works in the field of visualization, integrated methods that combine advanced visualization and/or interaction with data mining techniques in a principled way are rare. We present a framework based on constrained randomization which lets users explore high-dimensional data via ‘subjectively informative’ two-dimensional data visualizations. The user is presented with ‘interesting’ projections, allowing users to express their observations using visual interactions that update a background model representing the user's belief state. This background model is then considered by a projection-finding algorithm employing data randomization to compute a new ‘interesting’ projection. By providing users with information that contrasts with the background model, we maximize the chance that the user encounters striking new information present in the data. This process can be iterated until the user runs out of time or until the difference between the randomized and the real data is insignificant. We present two case studies, one controlled study on synthetic data and another on census data, using the proof-of-concept tool SIDE that demonstrates the presented framework.
Poisson’s Ratio and Young’s Modulus of Lipid Bilayers in Different Phases

A general computational method is introduced to estimate the Poisson’s ratio for membranes with small thickness. In this method, the Poisson’s ratio is calculated by utilizing a rescaling of inter-particle distances in one lateral direction under periodic boundary conditions. As an example for the coarse grained lipid model introduced by Lenz and Schmid, we calculate the Poisson’s ratio in the gel, fluid, and interdigitated phases. Having the Poisson’s ratio, enable us to obtain the Young’s modulus for the membranes in different phases. The approach may be applied to other membranes such as graphene and tethered membranes in order to predict the temperature dependence of its Poisson’s ratio and Young’s modulus.
Developing a Biomedical Expert Finding System Using Medical Subject Headings

Objectives Efficient identification of subject experts or expert communities is vital for the growth of any organization. Most of the available expert finding systems are based on self-nomination, which can be biased, and are unable to rank experts. Thus, the objective of this work was to develop a robust and unbiased expert finding system which can quantitatively measure expertise. Methods Medical Subject Headings (MeSH) is a controlled vocabulary developed by the National Library of Medicine (NLM) for indexing research publications, articles and books. Using the MeSH terms associated with peer-reviewed articles published from India and indexed in PubMed, we developed a Web-based program which can be used to identify subject experts and subjects associated with an expert. Results We have extensively tested our system to identify experts from India in various subjects. The system provides a ranked list of experts where known experts rank at the top of the list. The system is general; since it uses information available with the PubMed, it can be implemented for any country. Conclusions The expert finding system is able to successfully identify subject experts in India. Our system is unique because it allows the quantification of subject expertise, thus enabling the ranking of experts. Our system is based on peer-reviewed information. Use of MeSH terms as subjects has standardized the subject terminology. The system matches requirements of an ideal expert finding system.
Joint acute toxicity of diazinon and ammonia to Ceriodaphnia dubia

Dazinon is an organophosphorous pesticide widely found in municipal effluents as well as in agricultural and urban storm‐water discharges. Ammonia is frequently also present in such effluents as a consequence of bacterial degradation of organic material. Because these two contaminants may occur concurrently, their relationship with respect to joint toxicity is of interest, particularly in regard to interpreting the results of effluent tests and subsequent toxicity identification evaluations (TIEs). In this particular case, we obtained an effluent sample that exhibited toxicity to Ceriodaphnia dubia. Toxicity identification evaluations manipulations suggested that ammonia (40 mg/L as total NH3) and diazinon (0.75 μg/L) both contributed to toxicity. As part of the Phase 3 confirmation studies, an independent investigation was conducted to evaluate the interactions between these two toxicants using static tests that incorporated a 48‐h exposure period. Chemical concentrations were verified analytically. Mortalities were measured at 24‐h intervals and joint toxicity calculated on the basis of toxic units (TUs) for each toxicant. The 48‐h LC50 values (lethal concentrations for 50% of the population) for the individual chemicals averaged 0.36 μg/L and 1.11 mg/L for diazinon and un‐ionized ammonia, respectively. Under the assumption of strict additivity, the sum of TUs contributed by each toxicant at the LC50 of the mixture should total unity. The TUs associated with the mixtures in laboratory water averaged 1.37 and 1.47, respectively, for 24‐ and 48‐h exposure intervals. These results were similar to those obtained with the actual effluent sample and suggest that diazinon and ammonia exhibit less than additive toxicity when present together.
Effects of cilostamide and forskolin on the meiotic resumption and embryonic development of immature human oocytes.

BACKGROUND In an attempt to allow for acquisition of oocyte cytoplasmic maturation, PDE3 specific inhibitor, cilostamide and adenylate cyclase activator, forskolin were used to extend pre-maturation culture of immature human oocytes. METHODS Cumulus-oocyte complexes retrieved from unstimulated ovaries were continuously cultured under 20 microM cilostamide or 50 microM forskolin, alone or in combination for 6, 12, 24 or 48 h, respectively. Levels of intercellular gap junction communication (GJC) and maturational status were examined at these designated time points. Metaphase II oocytes obtained following 54 h biphasic culture (with meiotic inhibitors from 0 to 24 h, no meiotic inhibitors from 24 to 54 h) were subject to intracytoplasmic sperm injection and embryos were cultured for five more days. RESULTS Both cilostamide and forskolin delayed spontaneous meiotic progression after continuous culture with immature human oocytes. Combined treatment of cilostamide and forskolin significantly lowered the rates of germinal vesicle breakdown (GVBD) at 6, 12, 24 or 48 h after meiotic inhibitory culture, when compared with the control (all P < 0.05). A delay of 6 h for the loss of GJC was also observed under the combined treatment of cilostamide and forskolin. The fertilization rate was significantly higher under the combined treatment of cilostamide and forskolin than that of the control. Although the rates of oocyte maturation and embryo cleavage were similar among groups, there was a slight but non-significant increase in blastocyst formation rate with the treatment of cilostamide and forskolin. CONCLUSIONS Combined treatment of cilostamide and forskolin positively influences oocyte developmental competence by exhibiting a synergistic effect on the prevention of GJC loss and resumption of meiosis.
Membrane protein topology: effects of delta mu H+ on the translocation of charged residues explain the ‘positive inside’ rule.

The membrane electrochemical potential is critical for the export of most periplasmic proteins in Escherichia coli. Its exact role during insertion of integral inner membrane proteins, however, remains obscure. Using derivatives of the inner membrane protein leader peptidase (Lep), we now show that the membrane potential appears to stimulate the membrane translocation of chain segments containing negatively charged residues, that positively charged regions appear to be more easily translocated in the absence of a potential, and that certain Lep constructs insert with different topologies in the presence and absence of a membrane potential, suggesting that the electrochemical potential introduces an asymmetry between the topological effects of positively and negatively charged amino acids during the process of membrane protein insertion in E. coli.
Subjective cognition and amyloid deposition imaging: a Pittsburgh Compound B positron emission tomography study in normal elderly individuals.

OBJECTIVE To study the relationship between subjective cognition and the neuropathological hallmark of Alzheimer disease (AD), amyloid-β (Aβ) deposition, using carbon 11-labeled Pittsburgh Compound B (PiB) positron emission tomography in normal elderly individuals. DESIGN Cross-sectional analysis. SUBJECTS Forty-eight cognitively normal elderly subjects (11 with high PiB uptake and 28 with low PiB uptake) were included. All underwent clinical and neuropsychological evaluations, magnetic resonance imaging, and positron emission tomography. SETTING Berkeley Aging Cohort Study. MAIN OUTCOME MEASURE Relationship between PiB uptake and subjective cognition measures. RESULTS Subjects with high PiB uptake showed significantly lower performance than those with low PiB uptake on an episodic memory measure and were less confident about their general memory abilities when required to evaluate themselves relative to other people of the same age. High and low PiB uptake groups did not differ on the accuracy of their cognitive self-reports compared with objective cognitive performance. General memory self-reports from the whole group were significantly correlated with regional PiB uptake in the right medial prefrontal cortex and anterior cingulate cortex and in the right precuneus and posterior cingulate cortex. Reduced confidence about memory abilities was associated with greater PiB uptake in these brain regions. All results were independent of demographic variables and depressive affects. CONCLUSIONS A decrease of self-confidence about memory abilities in cognitively normal elderly subjects may be related to the neuropathological hallmark of AD measured with PiB-positron emission tomography. Subjective cognitive impairment may represent a very early clinical manifestation of AD.
Genome-wide linkage screen of a consanguineous multiple sclerosis kinship

Multiple sclerosis (MS), like A lzheimer’s disease (A D) and Parkinson’s disease (PD), is a common neurological disorder thought to be caused by the interaction of several genes with unknown environmental factors. In both A D and PD the identification of disease forms inherited in a classic Mendelian fashion has helped investigators elucidate pathogenetic mechanisms. In this study a whole-genome screen, with an average of 608 successful genotypes per person, was performed on nine members of a consanguineous family: the index case, three of her siblings and her daughter, all of whom have been diagnosed with definite MS; as well as the parents of the index case (first cousins), one of her five healthy siblings and her husband (who is also her first cousin). Nonparametric linkage analysis was performed on genotyping data. Based on the presence of consanguinity, the a priori hypothesis was that the disease is transmitted in an autosomal recessive fashion in the pedigree. Linkage analysis revealed a suggestive logarithm of odds (LO D) score of 2.29 on the long arm of chromosome 9. Four of five affected family members were identically homozygous for a haplotype under this peak, spanning approximately 43 cM, while the fifth affected subject and all unaffected family members were hetero zygous for the haplotype.