Miracle-dz/UniFAR-FTUs huggingface dataset:
An IFN-γ–stimulated ATF6–C/EBP-β–signaling pathway critical for the expression of Death Associated Protein Kinase 1 and induction of autophagy

The IFN family of cytokines operates a frontline defense against pathogens and neoplastic cells in vivo by controlling the expression of several genes. The death-associated protein kinase 1 (DAPK1), an IFN-γ–induced enzyme, controls cell cycle, apoptosis, autophagy, and tumor metastasis, and its expression is frequently down-regulated in a number of human tumors. Although the biochemical action of DAPK1 is well understood, mechanisms that regulate its expression are unclear. Previously, we have shown that transcription factor C/EBP-β is required for the basal and IFN-γ–induced expression of DAPK1. Here, we show that ATF6, an ER stress-induced transcription factor, interacts with C/EBP-β in an IFN-stimulated manner and is obligatory for Dapk1 expression. IFN-stimulated proteolytic processing of ATF6 and ERK1/2-mediated phosphorylation of C/EBP-β are necessary for these interactions. More importantly, IFN-γ failed to activate autophagic response in cells lacking either ATF6 or C/EBP-β. Consistent with these observations, the Atf6−/− mice were highly susceptible to lethal bacterial infections compared with the wild-type mice. These studies not only unravel an IFN signaling pathway that controls cell growth and antibacterial defense, but also expand the role of ATF6 beyond ER stress.
Karyotype differentiation in Chromaphyosemion killifishes (Cyprinodontiformes, Nothobranchiidae). III: Extensive karyotypic variability associated with low mitochondrial haplotype differentiation in C. bivittatum

We investigated chromosomal evolution in the African killifish species Chromaphyosemion bivittatum using a combination of cytogenetic and phylogenetic methods. Specimens from five populations were examined by conventional Giemsa staining as well as sequential chromosome banding with 4′,6-diamidino-2-phenylindole (DAPI), chromomycin A3 (CMA3), AgNO3-staining and C-banding. The cytogenetic analysis revealed variability in 2n ranging from 2n = 29 to 2n = 36 and in NF ranging from NF = 38 to NF = 44. Two populations showed an extensive chromosomal polymorphism (2n = 29–34, NF = 44 and 2n = 32–34, NF = 38–42, respectively). Karyotypic variability within and among populations was mainly due to Robertsonian translocations and heterochromatin additions, and chromosome banding patterns suggested that both types of chromosomal rearrangements were related to the presence of AT-rich heterochromatin. A phylogenetic analysis of the partial mitochondrial (mt) cytochrome b gene, using specimens from eleven populations, revealed a low degree of haplotype differentiation, which suggested a relatively recent divergence of the populations examined. This finding conformed to the low degree of morphological differentiation observed among C. bivittatum populations and might indicate fast chromosomal evolution. The high karyotypic variability may be caused by an elevated chromosomal mutation rate as well as certain aspects of the mating system and population dynamics of C. bivittatum facilitating the fixation of new chromosomal variants.
The impact factor and psychiatry journals: an international perspective

The impact factor (IF) is a metric for assessing academic journals. Despite its shortcomings, the IF is the preeminent yardstick by which the quality of scientific journals is determined. In this paper, the key aspects of the IF are covered from an international perspective, with a specific emphasis on psychiatry journals.
Sequential Interchange of Four Amino Acids from Blood Group B to Blood Group A Glycosyltransferase Boosts Catalytic Activity and Progressively Modifies Substrate Recognition in Human Recombinant Enzymes*

The human blood group A and B glycosyltransferase enzymes are highly homologous and the alteration of four critical amino acid residues (Arg-176 → Gly, Gly-235 → Ser, Leu-266 → Met, and Gly-268 → Ala) is sufficient to change the enzyme specificity from a blood group A to a blood group B glycosyltransferase. To carry out a systematic study, a synthetic gene strategy was employed to obtain their genes and to allow facile mutagenesis. Soluble forms of a recombinant glycosyltransferase A and a set of hybrid glycosyltransferase A and B mutants were expressed in Escherichia coli in high yields, which allowed them to be kinetically characterized extensively for the first time. A functional hybrid A/B mutant enzyme was able to catalyze both A and B reactions, with thek cat being 5-fold higher for the A donor. Surprisingly, even a single amino acid replacement in glycosyltransferase A with the corresponding residue from glycosyltransferase B (Arg-176 → Gly) produced enzymes with glycosyltransferase A activity only, but with very large (11-fold) increases in the k cat and increased specificity. The increases observed in k cat are among the largest obtained for a single amino acid change and are advantageous for the preparative scale synthesis of blood group antigens.
Major Histocompatibility Complex Class I Alleles Associated with Slow Simian Immunodeficiency Virus Disease Progression Bind Epitopes Recognized by Dominant Acute-Phase Cytotoxic-T-Lymphocyte Responses

ABSTRACT Certain major histocompatibility complex class I (MHC-I) alleles are associated with delayed disease progression in individuals infected with human immunodeficiency virus (HIV) and in macaques infected with simian immunodeficiency virus (SIV). However, little is known about the influence of these MHC alleles on acute-phase cellular immune responses. Here we follow 51 animals infected with SIVmac239 and demonstrate a dramatic association between Mamu-A*01 and -B*17 expression and slowed disease progression. We show that the dominant acute-phase cytotoxic T lymphocyte (CTL) responses in animals expressing these alleles are largely directed against two epitopes restricted by Mamu-A*01 and one epitope restricted by Mamu-B*17. One Mamu-A*01-restricted response (Tat28-35SL8) and the Mamu-B*17-restricted response (Nef165-173IW9) typically select for viral escape variants in early SIVmac239 infection. Interestingly, animals expressing Mamu-A*1 and -B*17 have less variation in the Tat28-35SL8 epitope during chronic infection than animals that express only Mamu-A*01. Our results show that MHC-I alleles that are associated with slow progression to AIDS bind epitopes recognized by dominant CTL responses during acute infection and underscore the importance of understanding CTL responses during primary HIV infection.
Temperature Mapping using the water proton chemical shift: A chemical shift selective phase mapping method

A proton‐chemical‐shift‐based temperature imaging method, called chemical shift selective phase mapping, is proposed. The technique uses frequency‐selective suppression to provide frequency selectivity to the phase mapping method. Separate imaging of the phase distributions of the water and nonwater signals reduced the error due to the presence of a nonwater signal in measuring the water proton chemical shift change in two‐component samples. Imaging of the phase difference between water and oil yielded an internally referenced water proton chemical shift measurement to visualize the temperature change distribution, which was unaffected by motion‐induced susceptibility changes.
Routing Networks: Adaptive Selection of Non-linear Functions for Multi-Task Learning

Multi-task learning (MTL) with neural networks leverages commonalities in tasks to improve performance, but often suffers from task interference which reduces the benefits of transfer. To address this issue we introduce the routing network paradigm, a novel neural network and training algorithm. A routing network is a kind of self-organizing neural network consisting of two components: a router and a set of one or more function blocks. A function block may be any neural network - for example a fully-connected or a convolutional layer. Given an input the router makes a routing decision, choosing a function block to apply and passing the output back to the router recursively, terminating when a fixed recursion depth is reached. In this way the routing network dynamically composes different function blocks for each input. We employ a collaborative multi-agent reinforcement learning (MARL) approach to jointly train the router and function blocks. We evaluate our model against cross-stitch networks and shared-layer baselines on multi-task settings of the MNIST, mini-imagenet, and CIFAR-100 datasets. Our experiments demonstrate a significant improvement in accuracy, with sharper convergence. In addition, routing networks have nearly constant per-task training cost while cross-stitch networks scale linearly with the number of tasks. On CIFAR-100 (20 tasks) we obtain cross-stitch performance levels with an 85% reduction in training time.
Detection of Cancer in Pap smear Cytological Images Using Bag of Texture Features

We present a visual dictionary based method for content based image retrieval in cervical microscopy images using texture features. The nucleus region in each image is identified by a simple and reliable segmentation algorithm and texture features are extracted from blocks of the region. These features from the entire database are clustered to build a visual dictionary. The histogram of the visual words present in an image is used as the representation of the image. Histogram intersection serves as the distance measure to do content based image retrieval. Experiments were conducted for various block sizes and number of clusters and the results are presented. The task was to identify images of cancerous cells from normal ones. The method offers encouraging results to utmost 90% accuracy. A brief discussion of the results and possible future directions are given
Icosandrin, a novel peltogynoid from the fruits of Phytolacca icosandra (Phytolaccaceae)

Besides the known compounds ( ± ) 3,3-bis-demethylpinoresinol (2), americanol A (3), spergulagenic acid (4), epi-acetylaleuritolic acid (5), 6′-palmityl-α-spinateryl-d-glucoside (6a) and 6′-palmityl-δ7-stigmastenyl-d-glucoside (6b), a novel peltogynoid (1) named icosandrin was obtained from the dried fruits of Phytolacca icosandra. This new compound was characterised by 1D-/2D-NMR, UV, IR and HR-MS techniques as 11ξ-methoxy-6,7-methylenedioxy-[2]benzopyrano-[4,3-b][1]-benzopyran-4-one. Toxicity of 1 was assessed through the Brine Shrimp Lethality Assay. Lignan 2 is reported for the first time in Phytolaccaceae family.
A low cost high sensitivity CMOS MEMS gas sensor

A CMOS micromachined gas with advantages of CMOS standard process and high sensitivity is presented in this paper. The proposed gas sensor was built with array of floating membranes and serially connected over an etched cavity. Finger type electrodes are built for sensing the resistance of coated sensor material. A proposed highly integrated multi-layer structure of electrodes is formed with metal/via layers in series to derive a lower and stable resistance of sensing material. The micro heater of n-type polysilicon with 4.2 kΩ is situated beneath each active area of the membrane to obtain a stable working temperature with an 120µW power consumption. The sensing material SnO2 was deposited onto the electrodes after sol-gel formation. Furthermore, the samples are fabricated by TSMC 0. 35µm 2P4M CMOS process which is provided by CIC with outstanding strong structures and high sensing performance with the minimum CO concentration under 4ppm. The experimental measurement shows the research is applicable for a low cost CO sensor with enough sensitivity.
An essential role for phoP in Mycobacterium tuberculosis virulence

Two‐component regulatory proteins function in bacteria as sensory and adaptive factors in response to a wide range of environmental stimuli. Some two‐component systems, such as PhoP/PhoQ, control transcription of key virulence genes essential for survival in host cells in diverse intracellular bacterial pathogens, including Salmonella sp. , Shigella sp. and Yersinia sp. In this study, we have disrupted the phoP gene from Mycobacterium tuberculosis, which codes for a putative transcription regulator factor of the two‐component system PhoP/PhoR. The phoP mutant strain exhibited impaired multiplication when cultured in mouse bone marrow‐derived macrophages. However, the mutation did not appear to affect survival of the organisms adversely inside macrophages. The mutant strain was also attenuated in vivo in a mouse infection model, with impaired growth observed in the lungs, livers and spleens. The results suggest that the phoP gene is required for intracellular growth of M. tuberculosis but is not essential for persistence of the bacilli.
Localization of CGRP receptor components and receptor binding sites in rhesus monkey brainstem: A detailed study using in situ hybridization, immunofluorescence, and autoradiography

Functional imaging studies have revealed that certain brainstem areas are activated during migraine attacks. The neuropeptide calcitonin gene–related peptide (CGRP) is associated with activation of the trigeminovascular system and transmission of nociceptive information and plays a key role in migraine pathophysiology. Therefore, to elucidate the role of CGRP, it is critical to identify the regions within the brainstem that process CGRP signaling. In situ hybridization and immunofluorescence were performed to detect mRNA expression and define cellular localization of calcitonin receptor–like receptor (CLR) and receptor activity–modifying protein 1 (RAMP1), respectively. To define CGRP receptor binding sites, in vitro autoradiography was performed with [3H]MK‐3207 (a CGRP receptor antagonist). CLR and RAMP1 mRNA and protein expression were detected in the pineal gland, medial mammillary nucleus, median eminence, infundibular stem, periaqueductal gray, area postrema, pontine raphe nucleus, gracile nucleus, spinal trigeminal nucleus, and spinal cord. RAMP1 mRNA expression was also detected in the posterior hypothalamic area, trochlear nucleus, dorsal raphe nucleus, medial lemniscus, pontine nuclei, vagus nerve, inferior olive, abducens nucleus, and motor trigeminal nucleus; protein coexpression of CLR and RAMP1 was observed in these areas via immunofluorescence. [3H]MK‐3207 showed high binding densities concordant with mRNA and protein expression. The present study suggests that several regions in the brainstem may be involved in CGRP signaling. Interestingly, we found receptor expression and antagonist binding in some areas that are not protected by the blood–brain barrier, which suggests that drugs inhibiting CGRP signaling may not be able to penetrate the central nervous system to antagonize receptors in these brain regions. J. Comp. Neurol. 524:90–118, 2016. © 2015 Wiley Periodicals, Inc.
High genetic diversity and population differentiation in Boechera fecunda, a rare relative of Arabidopsis

Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single‐copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to its widespread congener, Boechera stricta, which shares similar life history and mating system. Despite its rarity, B. fecunda had levels of genetic diversity similar to B. stricta for both microsatellites and nucleotide polymorphism. Populations of B. fecunda are highly differentiated, with a majority of genetic diversity existing among populations (FST = 0.57). Differences in molecular diversity and allele frequencies between western and eastern population groups suggest they experienced very different evolutionary histories.
3D frame synchronization detection based on classified epipolar geometry parameters

Nowadays, the stereoscopic 3D (S3D) has become more and more popular. However, sometimes people can still feel uncomfort when watching S3D videos. This phenomenon, to some extent, comes from the non-synchronization of the left and right views. That is, when a S3D videos is shot by two individual cameras, the left frames can't match exactly with their corresponding right frames in time domain. If the frame synchronization could not be ensured between the left and right views, extra disparity would be introduced due to different motion objects in the video content, which may cause visual fatigue. In this paper, we propose a temporal frame synchronization detection method, which adopts classified epipolar geometry parameters. The epipolar geometry parameters are estimated by classified keypoints pair sets. The keypoints are obtained by SIFT algorithm on two views, and then classified based on the difference about motion features. Experimental results show that, in many different types of scenes, the proposed method works well in the S3D frame synchronization detection.
Therapeutic effectiveness of novel 5‐fluorouracil‐loaded poly(methylidene malonate 2.1.2)‐based microspheres on F98 glioma‐bearing rats

Drug delivery to the central nervous system (CNS) remains a real challenge for neurosurgeons and neurologists, because many molecules cannot cross the blood‐brain barrier (BBB). In recent years, solid polymeric materials have been implanted into animal and human brains either by surgery or using stereotactic methods to assure the controlled release of a drug over a determined period, thus circumventing the difficulties posed by the BBB. Poly(methylidene malonate 2.1.2) (PMM 2.1.2) is a new polymer that was described a few years ago and that allows the fabrication of novel, 5‐fluorouracil (5‐FU)‐loaded PMM 2.1. 2 microspheres. The objective of the current study was to assess the therapeutic effectiveness of those particles in a rat brain tumor model, the F98 glioma.
Brief Alcohol Interventions and Multiple Risk Factors in Primary Care

Early identification and intervention of harmful/hazardous drinking in primary care are U.S. healthcare priorities. Traditionally, research has focused on designing interventions for patients in primary care who report hazardous/harmful alcohol use, even though it is likely for a patient to be at risk for multiple problems. This article has three major goals: (1) to present data highlighting the prevalence and co-variation of other risk factors with hazardous/harmful drinking, including data from a small descriptive study; (2) to review the literature on brief alcohol interventions designed to address multiple risk factors; and (3) to provide recommendations for future research. Despite data indicating primary care patients present with multiple risk factors, only a limited number of studies in the literature have investigated brief interventions addressing alcohol use and other risk factors. It is important for future research to expand brief alcohol interventions to include other risk factors as well.
Rapid and sensitive detection of Escherichia coli O157:H7 in bovine faeces by a multiplex PCR

Y. HU, Q. ZHANG and J.C. MEITZLER.1999. Cattle are considered the major reservoir for Escherichia coli O157:H7, one of the newly emerged foodborne human pathogens of animal origin and a leading cause of haemorrhagic colitis in humans. A sensitive test that can accurately and rapidly detect the organism in the food animal production environment is critically needed to monitor the emergence, transmission, and colonization of this pathogen in the animal reservoir. In this study, a novel multiplex polymerase chain reaction (PCR) assay was developed by using 5 sets of primers that specifically amplify segments of the eaeA, slt‐I, slt‐II, fliC, rfbE genes, which allowed simultaneous identification of serotype O157:H7 and its virulence factors in a single reaction. Analysis of 82 E. coli strains (49 O157:H7 and 33 non‐O157:H7) demonstrated that this PCR system successfully distinguished serotype O157:H7 from other serotypes of E. coli and provided accurate profiling of the shiga‐like toxins and the intimin adhesin in individual strains. This multiplex PCR assay did not cross‐react with the background bacterial flora in bovine faeces and could detect a single O157:H7 organism per gram of faeces when combined with an enrichment step. Together, these results indicate that the multiplex PCR assay can be used for specific identification and profiling of E. coli O157:H7 isolates, and may be applied to rapid and sensitive detection of E. coli O157:H7 in bovine faeces when combined with an enrichment step.
A three-phase boost-type grid-connected inverter based on synchronous reference frame control

In this paper, a synchronous reference frame (SRF) controlled three-phase boost-type grid-connected inverter with Current Space Vector Modulation (CSVM) is proposed for alternative energy sources regenerations. The averaged model of the equivalent boost-type inverter on SRF is derived in this paper. With the proposed averaged model, a SRF-PI compensator is analyzed with Bode diagram in frequency domain. Hence, the steady-state error tracking of the current can be effectively eliminated and power factor of the inverter can be well controlled under the decoupled d-q SRF control strategies. The feasibility of the proposed control scheme is verified by experimental results of a 700VA laboratory prototype.
Volumetric and interfacial inhomogeneities of random semi-infinite media: A unified perturbative scattering model

We propose a comprehensive analysis for the evaluation of the scattering from randomly inhomogeneous semi-infinite media, including both interfacial roughness and volume inhomogeneities, by applying the methodological approach of the Volumetric Perturbative Reciprocal Theory (VPRT). An unifying perspective on the scattering phenomenon considered in its entirety is gained and an analytic scattering model is obtained.
Ultra-low-power SiGe HBT technology for wide-range microwave applications

Ultra-low power SiGe HBT was developed for wide-range microwave applications. The key technologies of the SiGe HBT are based on well-controlled SiGe / Si epitaxial growth techniques with low-temperature chemical vapor deposition (CVD), which give several important features of the low-power SiGe HBT. The prominent features are a robustly designed n<sup>+</sup>-n<sup>-</sup>-p<sup>+</sup> emitter-base junction and a narrow base, realized by an epitaxially grown emitter and a low-temperature thermal cleaning prior to the emitter growth. These features were found to decrease both an emitter junction capacitance (C<sub>JE</sub>) and a carrier transit time in base (tau<sub>B</sub>) in a great extent. The low-temperature CVD also contributed to the reduction of a collector junction capacitance (C<sub>JC</sub>) by controlling a mono-poly interface in the collector. The effective decrease of C<sub>JE</sub>, tau<sub>B</sub>, and C<sub>JC</sub> has increased a cutoff frequency (f<sub>T</sub>) at a wide range of a collector current density (J<sub>C</sub>). As a result, Jc of the SiGe HBT decreased more than 60% compared to published data, at a wide f<sub>T</sub> range from 30 to 200 GHz.