Miracle-dz/UniFAR-FTUs huggingface dataset:
ICESsuHN105, a Novel Multiple Antibiotic Resistant ICE in Streptococcus suis Serotype 5 Strain HN105

Streptococcus suis serotype 5, an emerging zoonosis bacterial pathogen, has been isolated from infections in both pigs and humans. In this study, we sequenced the first complete genome of a virulent, multidrug-resistant SS5 strain HN105. The strain HN105 displayed enhanced pathogenicity in zebrafish and BABL/c mouse infection models. Comparative genome analysis identified a novel 80K integrative conjugative element (ICE), ICESsuHN105, as required for the multidrug resistance phenotype. Six corresponding antibiotic resistance genes in this ICE were identified, namely tet (O), tet (M), erm (two copies), aph, and spc. Phylogenetic analysis classified the element as a homolog of the ICESa2603 family, containing the typical family backbone and insertion DNA. DNA hybrids mediated by natural transformation between HN105 and ZY05719 verified the antibiotic resistant genes of ICESsuHN105 that could be transferred successfully, while they were dispersedly inserted with a single gene in different genomic locations of ZY05719(HN105) transformants. To further identify the horizontal transfer of ICESsuHN105 as a whole mobile genetic element, a circular intermediate form of ICESsuHN105 was detected by PCR. However, the effective conjugation using serotype 2 S. suis as recipients was not observed in current assays in vitro. Further studies confirmed the presence of the complete lantibiotic locus encoded in ICESsuHN105 that effectively inhibits the growth of other streptococci. In summary, this study demonstrated the presence of antibiotic resistance genes in ICE that are able to transfer between different clinical isolates and adapt to a broader range of Streptococcus serotype or species.
Using the loop chain abstraction to schedule across loops in existing code

Exposing opportunities for parallelisation while explicitly managing data locality is the primary challenge to porting and optimising computational science simulation codes to improve performance. OpenMP provides mechanisms for expressing parallelism, but it remains the programmer's responsibility to group computations to improve data locality. The loop chain abstraction, where a summary of data access patterns is included as pragmas associated with parallel loops, provides compilers with sufficient information to automate the parallelism versus data locality trade-off. We present the syntax and semantics of loop chain pragmas for indicating information about loops belonging to the loop chain and specification of a high-level schedule for the loop chain. We show example usage of the pragmas, detail attempts to automate the transformation of a legacy scientific code written with specific language constraints to loop chain codes, describe the compiler implementation for loop chain pragmas, and exhibit performance results for a computational fluid dynamics benchmark.
NOMA Inspired Cooperative Relaying System Using an AF Relay

In this letter, we propose a cooperative relaying system (CRS) based on non-orthogonal multiple access (NOMA) which uses an amplify-and-forward relay. This letter proposes a novel detection scheme in which the received signals of two consecutive time slots at destination is applied. We calculate asymptotic outage probability and derive diversity order of two for each symbol. Simulations show that our system has much better outage performance than NOMA-based CRS with decode-and-forward (DF) relay. Also, asymptotic ergodic sum rate increases log-linearly with transmit SNR and outperforms NOMA-based CRS with DF relay and conventional CRS. Finally, we verify analytical results by Monte-Carlo simulations.
Fast training of adaptive structural learning method of deep learning for multi modal data

Recently, deep learning has been applied in the techniques of artificial intelligence. Especially, their new architectures performed good results in the field of image recognition. However, the method is required to train not only image data, but also numerical data, text data, and other binary data. Multi modal data consists of two or more kinds of data such as a pair of image and text of giving an explanation of the image. The arrangement of multi modal data in the traditional method is formed in the squared array with no specification. In this paper, the method can modify the squared array of the multi modal data, according to the similarity of input-output pattern of adaptive structural learning method of deep belief network. Some experimental results show that the computational time of deep learning decreases.
With New Memories Come New Challenges

The performance of a modern computer system is increasingly getting dictated by the performance of the memory system. As we pack more cores, more threads per core, and domain specific accelerators on the chip, the memory system must scale in both capacity and bandwidth to supply the data to all these computing units. For the past four decades, we have had mainly two technologies for building the components of the memory system: SRAM for caches and DRAM for main memories, and systems have been limited by the constraints of these two technologies. We are at a juncture where several new memory technologies are emerging that can overcome the limitations of conventional technologies and offer new features such as nonvolatility. However, with new technologies come new challenges and system designers will need innovative solutions to address these challenges in order to fully realize the benefits offered by the emerging technologies.
A Subset of CCL25-Induced Gut-Homing T Cells Affects Intestinal Immunity to Infection and Cancer

Protective immunity relies upon differentiation of T cells into the appropriate subtype required to clear infections and efficient effector T cell localization to antigen-rich tissue. Recent studies have highlighted the role played by subpopulations of tissue-resident memory (TRM) T lymphocytes in the protection from invading pathogens. The intestinal mucosa and associated lymphoid tissue are densely populated by a variety of resident lymphocyte populations, including αβ and γδ CD8+ intraepithelial T lymphocytes (IELs) and CD4+ T cells. While the development of intestinal γδ CD8+ IELs has been extensively investigated, the origin and function of intestinal CD4+ T cells have not been clarified. We report that CCR9 signals delivered during naïve T cell priming promote the differentiation of a population of α4β7+ IFN-γ-producing memory CD4+ T cells, which displays a TRM molecular signature, preferentially localizes to the gastrointestinal (GI) tract and associated lymphoid tissue and cannot be mobilized by remote antigenic challenge. We further show that this population shapes the immune microenvironment of GI tissue, thus affecting effector immunity in infection and cancer.
Emotional Memory in Post-traumatic Stress Disorder: A Systematic PRISMA Review of Controlled Studies

Background: Emotional memory is an adaptive process that improves the memorization of emotional events or stimuli. In Post-Traumatic Stress Disorder (PTSD), emotional memory may be altered, which in turn may affect symptoms. Having a clearer view of the processes of interaction between memory and emotional stimuli in PTSD may improve our knowledge of this disorder, and could create new therapeutic management tools. Thus, we performed a systematic review of the evidence of specific emotional memory in PTSD patients. Method: Following PRISMA guidelines, a systematic review of MEDLINE, PsycInfo, and ScienceDirect was undertaken to identify controlled studies on emotional memory that used cognitive tasks on PTSD patients. The initial research was conducted from June 2017 to July 2017, and search terms included: Post-Traumatic Stress Disorder; PTSD; emotional memory; emotion; emotional; memory; and episodic memory. Results: Eighteen studies reporting on 387 PTSD patients met the eligibility criteria. Among the studies selected, 11 observed specific memory processing in PTSD patients, such as a greater memorization of negative information, or a trend to false recognition of negative information. In addition, attentional and inhibition processing seem to play an important role in emotional memory in PTSD sufferers. Furthermore, other studies that did not find behavioral differences between PTSD and control groups nevertheless showed differences in both specific cerebral activities and neurohormone levels during emotional memory tasks. Conclusion: This review has several limitations, including a limited number of controlled studies, small sample sizes, different tasks and methods. Nevertheless, the results of this systematic review provide interesting information on emotional memory for clinicians and researchers, as they seem to highlight facilitated memory processing for negative information in PTSD patients. This topic needs further controlled studies with sensitive behavioral tasks. Also, future studies may evaluate emotional memory after symptom amelioration.
Channel Estimation in MIMO–OFDM Systems Based on a New Adaptive Greedy Algorithm

Channel estimation methods based on compressed sensing can be used to effectively obtain channel state information of MIMO-OFDM systems. This letter proposes a new adaptive matching pursuit (NAMP) algorithm and the evaluation prototype based on the LTE-Advanced wireless channel model. First, NAMP does not need the priori-knowledge of the sparsity level. Second, the fixed step size is determined in order to improve the efficiency of signal reconstruction. Third, a singular entropy order determination mechanism is employed to prevent the less relevant atoms from being introduced. Finally, simulation results are discussed in detail, which demonstrate that the proposed method results in lower computational complexity, and especially achieves more stable performance.
Rulers on Our Arms

In this article, we propose a mobile system, Aware, which turns our wearable or mobile device into a ruler. It can estimate the size of objects that could be large in size and not directly touchable by the user. Such a design will enable a rich set of applications that count on the size information of surrounding environments/objects. Aware purely utilizes the motion sensors on the device for object size measures. It can also integrate with the crowdsourcing feature for both performance improvement and result sharing. We propose a series of key techniques to address three major challenges in the Aware design: (1) user’s angle of line-of-sights to the object is used in the size measure but motion sensors track only the angle of arm’s waving, (2) motion sensors are noisy that require novel and effective data processing techniques, otherwise the errors could easily overwhelm the final result, and (3) in the crowdsourcing mode, Aware needs to identify vicinal objects of similar sizes and effectively fuse the measured sizes that correspond to the same object. We consolidate the above designs and implement Aware on Android platforms. Extensive experiments with four users show that Aware can achieve accurate measurement performance for the objects of various sizes in both indoor and outdoor environments.
Polyphenism – A Window Into Gene-Environment Interactions and Phenotypic Plasticity

Phenotypic plasticity describes the capacity of a single genotype to exhibit a variety of phenotypes as well as the mechanisms that translate environmental variation into reproducible phenotypic modifications. Polyphenism describes the unique sub-type of phenotypic plasticity where the outputs are not continuous, but rather discrete and multi-stable, resulting in several distinct phenotypes on the same genetic background. Epigenetic regulation underpins the stable phenotypic divergences that exemplify polyphenism and their evolutionary origin. Here, we briefly summarize the apparent ubiquity and diversity of polyphenisms across the animal kingdom. We briefly review the best characterized models across taxa and highlight the consistent themes both in their epidemiology and what little we know about molecular mechanisms. Finally, we highlight work that supports the possibility that humans may have a subtle polyphenism at the level of metabolism.
Therapeutic Inhibition of the Complement System in Diseases of the Central Nervous System

The complement system plays critical roles in development, homeostasis, and regeneration in the central nervous system (CNS) throughout life; however, complement dysregulation in the CNS can lead to damage and disease. Complement proteins, regulators, and receptors are widely expressed throughout the CNS and, in many cases, are upregulated in disease. Genetic and epidemiological studies, cerebrospinal fluid (CSF) and plasma biomarker measurements and pathological analysis of post-mortem tissues have all implicated complement in multiple CNS diseases including multiple sclerosis (MS), neuromyelitis optica (NMO), neurotrauma, stroke, amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Given this body of evidence implicating complement in diverse brain diseases, manipulating complement in the brain is an attractive prospect; however, the blood-brain barrier (BBB), critical to protect the brain from potentially harmful agents in the circulation, is also impermeable to current complement-targeting therapeutics, making drug design much more challenging. For example, antibody therapeutics administered systemically are essentially excluded from the brain. Recent protocols have utilized “Trojan horse” techniques to transport therapeutics across the BBB or used osmotic shock or ultrasound to temporarily disrupt the BBB. Most research to date exploring the impact of complement inhibition on CNS diseases has been in animal models, and some of these studies have generated convincing data; for example, in models of MS, NMO, and stroke. There have been a few recent clinical trials of available anti-complement drugs in CNS diseases associated with BBB impairment, for example the use of the anti-C5 monoclonal antibody (mAb) eculizumab in NMO, but for most CNS diseases there have been no human trials of anti-complement therapies. Here we will review the evidence implicating complement in diverse CNS disorders, from acute, such as traumatic brain or spine injury, to chronic, including demyelinating, neuroinflammatory, and neurodegenerative diseases. We will discuss the particular problems of drug access into the CNS and explore ways in which anti-complement therapies might be tailored for CNS disease.
Inhibitors of Human ABCG2: From Technical Background to Recent Updates With Clinical Implications

The ATP-binding cassette transporter G2 (ABCG2; also known as breast cancer resistance protein, BCRP) has been suggested to be involved in clinical multidrug resistance (MDR) in cancer like other ABC transporters such as ABCB1 (P-glycoprotein). As an efflux pump exhibiting a broad substrate specificity localized on cellular plasma membrane, ABCG2 excretes a variety of endogenous and exogenous substrates including chemotherapeutic agents, such as mitoxantrone and several tyrosine kinase inhibitors. Moreover, in the normal tissues, ABCG2 is expressed on the apical membranes and plays a pivotal role in tissue protection against various xenobiotics. For this reason, ABCG2 is recognized to be an important determinant of the pharmacokinetic characteristics of its substrate drugs. Although the clinical relevance of reversing the ABCG2-mediated MDR has been inconclusive, an appropriate modulation of ABCG2 function during chemotherapy should logically enhance the efficacy of anti-cancer agents by overcoming the MDR phenotype and/or improving their pharmacokinetics. To confirm this possibility, considerable efforts have been devoted to developing ABCG2 inhibitors, although there is no clinically available substance for this purpose. As a clue for addressing this issue, this mini-review provides integrated information covering the technical backgrounds necessary to evaluate the ABCG2 inhibitory effects on the target compounds and a current update on the ABCG2 inhibitors. This essentially includes our recent findings, as we serendipitously identified febuxostat, a well-used agent for hyperuricemia as a strong ABCG2 inhibitor, that possesses some promising potentials. We hope that an overview described here will add value to further studies involving in the multidrug transporters.
Understanding Diversity Ideologies From the Target's Perspective: A Review and Future Directions

We present a review of the diversity ideologies literature from the target's perspective. In particular, we focus on how diversity ideologies—beliefs or organizational practices with regards to how to approach diversity—affect racial minorities' and women's self-perceptions and experiences at work. This review suggests that a diversity aware ideology (i.e., multiculturalism) is more beneficial than a diversity blind ideology (i.e., colorblindness) for racial-ethnic minorities (e.g., better performance outcomes; more psychological engagement, inclusion, and workplace satisfaction; more positive leadership self-perceptions; and reduced perceptions of bias and turnover intentions). In contrast, for women, gender-blindness is associated with more positive outcomes than gender awareness (e.g., enhanced self-confidence, pro-active behaviors and leadership emergence). Importantly, multiculturalism and gender-blindness can both produce negative side effects for racial minorities and women, respectively, which highlights the importance of developing approaches to address the shortcomings of these conventional ideologies. We discuss the implications and offer recommendations for future research.
Temperature Modifies Consumer-Resource Interaction Strength Through Its Effects on Biological Rates and Body Mass

Temperature is the most significant environmental gradient at the global scale, impacting the distributions of species and their ecological interactions. It is now established that temperature affects several biological rates and body mass, and can, in turn, alter interaction strength. Latitudinal variation in the strength of interactions has been observed for trophic and competitive interactions and many studies support that biotic interactions are more intense at low latitudes. Nevertheless, the mechanisms underlying the temperature dependence of trophic regulation, the effect of consumers on their preys, remain unclear. The aim of our study is to get better insights on the effects of temperature on trophic regulation. We used a consumer-resource model and considered that organisms' biological rates present a unimodal thermal response and that body mass decreases with temperature. We compared three measures of interaction strength: per capita, per population and net interaction strength. Our results demonstrate that the effect of temperature on interaction strength is contingent upon which species’ biological rates are temperature dependent. When all biological rates are temperature dependent, the thermal response of interaction strength is hump-shaped following the scaling of search rate, whilst it is monotonically decreasing when only mortality rates vary with temperature. Finally, we show that temperature can indirectly impact trophic interaction strength through the temperature-size rule. A decrease in organisms' body size due to temperature induces a decrease in per capita and per population interaction strength and tend to decrease net interaction strength, depending on which trophic level follows the temperature-size rule. Our analysis gives an overview of how temperature, through various effects, may impact different measures of interaction strength.
Targeting uPAR by CRISPR/Cas9 System Attenuates Cancer Malignancy and Multidrug Resistance

Urokinase plasminogen activator receptor (uPAR), a member of the lymphocyte antigen 6 protein superfamily, is overexpressed in different types of cancers and plays an important role in tumorigenesis and development. In this study, we successfully targeted uPAR by CRISPR/Cas9 system in two human cancer cell lines with two individual sgRNAs. Knockout of uPAR inhibited cell proliferation, migration and invasion. Furthermore, knockout of uPAR decreases resistance to 5-FU, cisplatin, docetaxel, and doxorubicin in these cells. Although there are several limitations in the application of CRISPR/Cas9 system for cancer patients, our study offers valuable evidences for the role of uPAR in cancer malignancy and drug resistance.
Monstrous Moonshine and the Classification of CFT : (16 lectures given in Istanbul, August 1998)

In these notes, based on lectures given in Istanbul, we give an introduction both to Monstrous Moonshine and to the classification of rational conformal field theories, using this as an excuse to explore several related structures and go on a little tour of modern math. We will discuss Lie algebras, modular functions, the finite simple group classification, vertex operator algebras, Fermat's Last Theorem, category theory, (generalised) Kac-Moody algebras, denominator identities, the A-D-E meta-pattern, representations of affine algebras, Galois theory, etc. This work is informal and pedagogical, and aimed mostly at grad students in math or math phys, but I hope that many interested nonexperts will find something of value here -- like any good Walt Disney movie I try not to completely ignore the `grown-ups'. My emphasis is on ideas and motivations, so these notes are intended to complement other papers and books where this material is presented with more technical detail. The level of difficulty varies significantly from topic to topic. The two parts -- in fact any of the sections -- can be read independently.
Perampanel Affects Up-Stream Regulatory Signaling Pathways of GluA1 Phosphorylation in Normal and Epileptic Rats

To elucidate the pharmacological properties of perampanel [2-(2-oxo-1-phenyl-5-pyridin-2-yl-1,2-dihydropyridin-3-yl)benzonitrile, a novel non-competitive antagonist of AMPA receptor], we investigated its effects on the up-stream regulatory pathways of GluA1 phosphorylation including protein kinase C (PKC), Ca2+-calmodulin-dependent protein kinase II (CAMKII), protein kinase A (PKA), extracellular signal-regulated kinase 1/2 (ERK1/2), c-Jun N-terminal kinase (JNK), protein phosphatase (PP) 1, PP2A, and PP2B in normal and pilocarpine-induced epileptic rat model using Western blot analysis. In normal animals, perampanel affected GluA1 expression/phosphorylation, PKC, CAMKII, PKA, ERK1/2, JNK, and PPs activities. In epileptic rats, perampanel effectively inhibited spontaneous seizure activities. Perampanel enhanced phospho (p)-GluA1-S831 and -S845 ratios (phosphoprotein/total protein), while it reduced GluA1 expression. Perampanel also increased pCAMKII and pPKA ratios, which phosphorylate GluA1-S831 and -S845 site, respectively. Perampanel elevated pJNK and pPP2B ratios, which phosphorylates and dephosphorylates both GluA1-S831 and -S845 sits. Perampanel also increased pERK1/2 ratio in epileptic animals, while U0126 (an ERK1/2 inhibitor) did not affect pGluA1 ratios. Perampanel did not influence PKC, PP1, and PP2A expression levels and their phosphorylation ratios. In addition, perampanel did not have a detrimental impact on cognitive abilities of epileptic and normal rats in Morris water maze test. These findings suggest that perampanel may regulate AMPA receptor functionality via not only blockade of AMPA receptor but also the regulations of multiple molecules (CAMKII, PKA, JNK, and pPP2B)-mediated GluA1 phosphorylations without negative effects on cognition, although the effects of perampanel on PKC, PP1, and PP2A activities were different between normal and epileptic rats.