Miracle-dz/UniFAR-FTUs huggingface dataset:
Deletion of a Predicted β-Sheet Domain within the Amino Terminus of Herpes Simplex Virus Glycoprotein K Conserved among Alphaherpesviruses Prevents Virus Entry into Neuronal Axons

ABSTRACT We have shown previously that herpes simplex virus 1 (HSV-1) lacking expression of the entire glycoprotein K (gK) or expressing gK with a 38-amino-acid deletion (gKΔ31–68 mutation) failed to infect ganglionic neurons after ocular infection of mice. We constructed a new model for the predicted three-dimensional structure of gK, revealing that the gKΔ31–68 mutation spans a well-defined β-sheet structure within the amino terminus of gK, which is conserved among alphaherpesviruses. The HSV-1(McKrae) gKΔ31–68 virus was tested for the ability to enter into ganglionic neuronal axons in cell culture of explanted rat ganglia using a novel virus entry proximity ligation assay (VEPLA). In this assay, cell surface-bound virions were detected by the colocalization of gD and its cognate receptor nectin-1 on infected neuronal surfaces. Capsids that have entered into the cytoplasm were detected by the colocalization of the virion tegument protein UL37, with dynein required for loading of virion capsids onto microtubules for retrograde transport to the nucleus. HSV-1(McKrae) gKΔ31–68 attached to cell surfaces of Vero cells and ganglionic axons in cell culture as efficiently as wild-type HSV-1(McKrae). However, unlike the wild-type virus, the mutant virus failed to enter into the axoplasm of ganglionic neurons. This work suggests that the amino terminus of gK is a critical determinant for entry into neuronal axons and may serve similar conserved functions for other alphaherpesviruses. IMPORTANCE Alphaherpesviruses, unlike beta- and gammaherpesviruses, have the unique ability to infect and establish latency in neurons. Glycoprotein K (gK) and the membrane protein UL20 are conserved among all alphaherpesviruses. We show here that a predicted β-sheet domain, which is conserved among alphaherpesviruses, functions in HSV-1 entry into neuronal axons, suggesting that it may serve similar functions for other herpesviruses. These results are in agreement with our previous observations that deletion of this gK domain prevents the virus from successfully infecting ganglionic neurons after ocular infection of mice.
Leveraging specifications of subcomponents to mine precise specifications of composite components

Specifications play an important role in many software engineering activities. Despite their usefulness, formal specifications are often unavailable in practice. Specification mining techniques try to automatically recover specifications from existing programs. Unfortunately, mined specifications are often overly general, which hampers their applications in the downstream analysis and testing. Nowadays, programmers develop software systems by utilizing existing components that usually have some available specifications. However, benefits of these available specifications are not explored by current specification miners. In this paper, we propose an approach to leverage available specifications of subcomponents to improve the precision of specifications of the composite component mined by state-based mining techniques. We monitor subcomponents against their specifications during the mining process and use states that are reached to construct abstract states of the composite component. Our approach makes subcomponents' states encoded within their specifications visible to their composite component, and improves the precision of mined specifications by effectively increasing the number of their states. The empirical evaluation shows that our approach can significantly improve the precision of mined specifications by removing erroneous behavior without noticeable loss of recall.
Ammonium and Urea Transporter Inventory of the Selaginella and Physcomitrella Genomes

Ammonium and urea are important nitrogen sources for autotrophic organisms. Plant genomes encode several families of specific transporters for these molecules, plus other uptake mechanisms such as aquaporins and ABC transporters. Selaginella and Physcomitrella are representatives of lycophytes and bryophytes, respectively, and the recent completion of their genome sequences provided us with an opportunity for comparative genome studies, with special emphasis on the adaptive processes that accompanied the conquest of dry land and the evolution of a vascular system. Our phylogenetic analysis revealed that the number of genes encoding urea transporters underwent a progressive reduction during evolution, eventually down to a single copy in vascular plants. Conversely, no clear evolutionary pattern was found for ammonium transporters, and their number and distribution in families varies between species. In particular Selaginella, similar to rice, favors the AMT2/MEP family of ammonium transporters over the plant-specific AMT1 type. In comparison, Physcomitrella presents several members belonging to both families.
Digital compensation of chromatic dispersion in 112-Gbit/s PDM-QPSK system

High bit rates optical communication systems pose the challenge of their tolerance to linear and nonlinear fiber impairments. Coherent optical receivers using digital signal processing techniques can mitigate the fiber impairments in the optical transmission system, including the chromatic dispersion equalization with digital filters. In this paper, an adaptive finite impulse response filter employing normalized least mean square algorithm is developed for compensating the chromatic dispersion in a 112-Gbit/s polarization division multiplexed quadrature phase shift keying coherent communication system, which is established in the VPI simulation platform. The principle of the adaptive normalized least mean square algorithm for signal equalization is analyzed theoretically, and at the meanwhile, the taps number and the tap weights in the adaptive finite impulse response filter for compensating a certain fiber chromatic dispersion are also investigated by numerical simulation. The chromatic dispersion compensation performance of the adaptive filter is analyzed by evaluating the behavior of the bit-error-rate versus the optical signal-to-noise ratio, and the compensation results are also compared with other present digital filters.
Stigmatic exudate in the Annonaceae: Pollinator reward, pollen germination medium or extragynoecial compitum?

Abstract Although “dry‐type” stigmas are widely regarded as ancestral in angiosperms, the early‐divergent family Annonaceae has copious stigmatic exudate. We evaluate three putative functions for this exudate: as a nutritive reward for pollinators; as a pollen germination medium; and as an extragynoecial compitum that enables pollen tube growth between carpels. Stigmatic exudate is fructose dominated (72.2%), but with high levels of glucose and sucrose; the dominance of hexose sugars and the diversity of amino acids observed, including many that are essential for insects, support a nutritive role for pollinators. Sugar concentration in pre‐receptive flowers is high (28.2%), falling during the peak period of stigmatic receptivity (17.4%), and then rising again toward the end of the pistillate phase (32.9%). Pollen germination was highest in sugar concentrations <20%. Sugar concentrations during the peak pistillate phase therefore provide optimal osmolarity for pollen hydration and germination; subsequent changes in sugar concentration during anthesis reinforce protogyny (in which carpels mature before stamens), enabling the retention of concentrated exudate into the staminate phase as a pollinator food reward without the possibility of pollen germination. Intercarpellary growth of pollen tubes was confirmed: the exudate therefore also functions as a suprastylar extragynoecial compitum, overcoming the limitations of apocarpy.
The impact of synchronization in message passing while scaling multi-core MPSoC systems

Several previous works have already stressed the impact and importance of the performance of message passing directives for MPSoC platforms. In this paper we present a set of algorithms to perform synchronization in message-based communication in a multicore, NoC-based MPSoC environment. A scalable MPSoC architecture was implemented using SystemC, being composed by a set of MIPS cores available in Open-Cores. Data regarding the energy, contention and number of messages for each communication channel were collected. The data collected show differences in performance for the algorithms under different topologies. This suggests the necessity of properly choosing the most suitable synchronization algorithm for each combination of topology and workload. We also show how contention affects the communication resources of the platform.
The Ser82 RAGE Variant Affects Lung Function and Serum RAGE in Smokers and sRAGE Production In Vitro

Introduction Genome-Wide Association Studies have identified associations between lung function measures and Chronic Obstructive Pulmonary Disease (COPD) and chromosome region 6p21 containing the gene for the Advanced Glycation End Product Receptor (AGER, encoding RAGE). We aimed to (i) characterise RAGE expression in the lung, (ii) identify AGER transcripts, (iii) ascertain if SNP rs2070600 (Gly82Ser C/T) is associated with lung function and serum sRAGE levels and (iv) identify whether the Gly82Ser variant is functionally important in altering sRAGE levels in an airway epithelial cell model. Methods Immunohistochemistry was used to identify RAGE protein expression in 26 human tissues and qPCR was used to quantify AGER mRNA in lung cells. Gene expression array data was used to identify AGER expression during lung development in 38 fetal lung samples. RNA-Seq was used to identify AGER transcripts in lung cells. sRAGE levels were assessed in cells and patient serum by ELISA. BEAS2B-R1 cells were transfected to overexpress RAGE protein with either the Gly82 or Ser82 variant and sRAGE levels identified. Results Immunohistochemical assessment of 6 adult lung samples identified high RAGE expression in the alveoli of healthy adults and individuals with COPD. AGER/RAGE expression increased across developmental stages in human fetal lung at both the mRNA (38 samples) and protein levels (20 samples). Extensive AGER splicing was identified. The rs2070600T (Ser82) allele is associated with higher FEV1, FEV1/FVC and lower serum sRAGE levels in UK smokers. Using an airway epithelium model overexpressing the Gly82 or Ser82 variants we found that HMGB1 activation of the RAGE-Ser82 receptor results in lower sRAGE production. Conclusions This study provides new information regarding the expression profile and potential role of RAGE in the human lung and shows a functional role of the Gly82Ser variant. These findings advance our understanding of the potential mechanisms underlying COPD particularly for carriers of this AGER polymorphism.
Differences Between Patients With Schizophrenia With and Without Co-Occurring Methamphetamine Use Disorders in a Taiwanese Public Psychiatric Hospital

Abstract This study aimed to examine the factors related to and the outcomes of schizophrenic patients with co-occurring methamphetamine use disorders (MUDs). All schizophrenic patients discharged from a psychiatric hospital between January 1, 2006, and December 31, 2006, were monitored. This study compared the important demographic and clinical variables between patients with co-occurring MUDs and those without, and postdischarge measured time to rehospitalization during a 1-year period. Seven hundred fifty-six patients were included in this study. Of these patients, 88 (11.6%) reported the use of methamphetamine. Univariate analyses indicated that male sex, low educational level, discharge against medical advice, missed first appointment after discharge, co-occurring other illicit substance use disorder, age (younger), diazepam equivalents prescribed at discharge (higher), number of previous admissions within the past 5 years (higher), and length of hospital stay (longer) were predictive of patients with co-occurring MUDs. There were also significant differences in time to rehospitalization between these two groups during the follow-up periods. Many factors can be identified in schizophrenic patients with co-occurring MUDs. Furthermore, schizophrenic patients with co-occurring MUDs were more likely to be rehospitalized. Future studies in many different mental health systems are needed before these findings can be generalized.
Novel Cluster Formation Framework for Energy Efficient Short-Range Cooperative Strategies

Excessive energy consumption has been recognized as a number one problem that may weaken the growth in future communication networks. This means that the main effort of nowadays wireless communications research shall be moved to energy efficient solutions. One of the most interesting approaches to achieve energy efficiency is to enable the short-range cooperative strategies among multi-standard mobile devices. The short-range cooperative strategies are highly beneficial in terms of energy savings, as they shift the wireless communications paradigm from high power cellular interfaces to low power WPAN interfaces. Keeping this in mind, our proposed clustering framework builds a solid fundament to bring short-range cooperative strategies into the wireless world. The key features of our method are robustness, simplicity and reliability, which are achieved via novel mechanisms of silent association and discrimination of non-persistent neighbors. Herein we present the analysis of state of the art clustering designs, which is followed by the detailed description of the presented method along with the results, from WiMedia MAC ns-2 simulator, that verify principles of the proposed method.
Finite Difference Time Domain Analysis of Shielding Effectiveness of Wire-Mesh Reinforcement

A numerical method is presented for calculating shielding effectiveness of the wire-mesh reinforcement. The model is based on the field approximation for thin wire in the finite-difference time-domain (FDTD) method. Then, the proposed method is used to the analysis of shielding effectiveness of wire-mesh reinforcement. The FDTD results are in very good agreement with the results of the method of moment (MOM) and experimental results
A gene for isolated congenital ptosis maps to a 3-cM region within 1p32-p34.1.

Hereditary isolated congenital ptosis is an autosomal dominant disorder with incomplete penetrance characterized by a variable degree of unilateral or bilateral drooping of the upper eyelids. We report linkage of this disorder in a large family to markers on chromosome 1p. In our sample of 37 meioses, nine informative markers did not recombine with the disease. D1S2677 gave a maximum two-point LOD score of 8.8 on the assumption of 90% penetrance (theta = 0). D1S447/2733 and D1S1616 flank the disease locus, with two-point LOD scores of 5.6/6.6 (theta = .04) and 4.9 (theta = .05), respectively, defining a region of 2.8 cM. FISH of YACs containing flanking recombinant markers localizes the gene to chromosome 1p32-p34.1. These data establish a map location for an isolated congenital ptosis gene and demonstrate that this disorder is genetically distinct from other extraocular muscle-specific disorders such as congenital fibrosis of the extraocular muscles and blepharophimosis.
A single point mutation reveals gating of the human ClC-5 Cl−/H+ antiporter

• ClC‐5 is a 2Cl−/1H+ antiporter expressed in endosomes that is essential for proper endocytosis, but its molecular function is still not understood. • In heterologous systems ClC‐5 elicits currents only at positive potentials. This rectifying behaviour conflicts with most of the models proposed to explain ClC‐5 function. The origin of this rectification is unknown. • Here we identified a ClC‐5 mutation, D76H, that elicits inward tail currents at negative potentials. • These currents reflect transmembrane transport that preserve the 2Cl−/1H+ stoichiometry. • We conclude that a gating mechanism regulates ClC‐5 transport activity and is at least in part responsible for the strong rectification of ClC‐5 currents.
Annual research review: phenotypic and causal structure of conduct disorder in the broader context of prevalent forms of psychopathology.

BACKGROUND A better understanding of the nature and etiology of conduct disorder (CD) can inform nosology and vice versa. We posit that any prevalent form of psychopathology, including CD, can be best understood if it is studied in the context of other correlated forms of child and adolescent psychopathology using formal models to guide inquiry. METHODS Review of both cross-sectional and longitudinal studies of the place of CD in the phenotypic and causal structure of prevalent psychopathology, with an emphasis on similarities and differences between CD and oppositional defiant disorder (ODD). Papers were located using Web of Science by topic searches with no restriction on year of publication. RESULTS Although some important nosologic questions remain unanswered, the dimensional phenotype of CD is well defined. CD differs from other disorders in its correlates, associated impairment, and course. Nonetheless, it is robustly correlated with many other prevalent dimensions of psychopathology both concurrently and predictively, including both other 'externalizing' disorders and some 'internalizing' disorders. Based on emerging evidence, we hypothesize that these concurrent and predictive correlations result primarily from widespread genetic pleiotropy, with some genetic factors nonspecifically influencing risk for multiple correlated dimensions of psychopathology. In contrast, environmental influences mostly act to differentiate dimensions of psychopathology from one another both concurrently and over time. CD and ODD share half of their genetic influences, but their genetic etiologies are distinct in other ways. Unlike most other dimensions of psychopathology, half of the genetic influences on CD appear to be unique to CD. In contrast, ODD broadly shares nearly all of its genetic influences with other disorders and has little unique genetic variance. CONCLUSIONS Conduct disorder is a relatively distinct syndrome at both phenotypic and etiologic levels, but much is revealed by studying CD in the context of its causal and phenotypic associations with other disorders over time. Advancing and refining formal causal models that specify the common and unique causes and biological mechanisms underlying each correlated dimension of psychopathology should facilitate research on the fundamental nature and nosology of CD.
Incidence of chronic myeloproliferative disorders in the city of Göteborg, Sweden 1983–1992

Abstract: An estimation of the incidence of polycythaemia vera (PV), essential thrombocythaemia (ET) and chronic idiopathic myelofibrosis (CIM) in the city of Göteborg, Sweden during the period 1983–1992 was made from a retrospective case analysis of patients registered as chronic myeloproliferative disorders (CMPD) at the Departments of Medicine and the Department of Pathology of the two major hospitals in the city. A total of 125 cases of PV, 56 males and 69 females were identified. The number of cases as well as the age‐specific incidence increased with age. The over all annual gender‐specific incidence was 2.69 cases per 105 male inhabitants and 3.12 cases per 105 female inhabitants. The incidence of PV in relation to the European Standard Population was 2.02 cases per 105 inhabitants and year. There were 72 cases, 20 males and 52 females, with ET. The age‐specific incidence was in all ages higher for females than for males and increased with age. The annual gender‐specific incidence was 0.96 per 105 male inhabitants and 2.35 per 105 female inhabitants. The incidence of ET in relation to the European Standard Population was 1.28 per 105 persons and year. There were 20 cases of CIM, 11 males and 9 females. The annual gender‐specific incidence of CIM was 0.53/105 male inhabitants and 0.41/105 female inhabitants. The incidence of CIM in relation to the European Standard Population was 0.31 per 105 persons and year. Seven persons, 2 males and 5 females, had a CMPD that could not be included in any of the above‐mentioned groups, but were registered as CMPD, unclassified.
Is Job Performance better attributable to Performance Management System through Work Engagement

Managing performance of employees is a critical task for any organization. In this regard there is more emphasis on performance management and work engagement of the employees in the recent times. Performance management has its own niche in ensuring work engagement, which can in-turn lead to higher job performance. Performance management as a concept and practice has substantive potential to fulfil business demands of an organization by integrating its growth with motivational needs of human resource. The purpose of this paper is to reconnoitre the influence of performance management system (PMS)throughwork engagement on job performance. A total of 58 valid responses, as part of the pilot testare analysed to establish the theoretical robustnessof this study. It is found that PMSisbetter attributable to job performance only when it has a favourable influence on employees work attitude such as work engagement. Hence, PMS interventions have to first have a beneficial influence on employee attitudes like work engagement even before it exercises a significant positive influence on job performance. The study has implications for HR teams to revisit the PMS periodically to incorporate the evolving themes in an organization, wherein employees and organizations co-evolve.
Enriched environment restores hippocampal cell proliferation and ameliorates cognitive deficits in chronically stressed rats

Adult neurogenesis, particularly in the subgranular zone, is thought to be linked with learning and memory. Chronic stress inhibits adult hippocampal neurogenesis and also impairs learning and memory. On the other hand, exposure to enriched environment (EE) is reported to enhance the survival of new neurons and improve cognition. Accordingly, in the present study, we examined whether short‐term EE after stress could ameliorate the stress‐induced decrease in hippocampal cell proliferation and impairment in radial arm maze learning. After restraint stress (6 hr/day, 21 days) adult rats were exposed to EE (6 hr/day, 10 days). We observed that chronic restraint stress severely affected formation of new cells and learning. Stressed rats showed a significant decrease (70%) in the number of BrdU (5‐bromo‐2′‐deoxyuridine)‐immunoreactive cells and impairment in the performance of the partially baited radial arm maze task. Interestingly, EE after stress completely restored the hippocampal cell proliferation. On par with the restoration of hippocampal cytogenesis, short‐term EE after stress resulted in a significant increase in percentage correct choices and a decrease in the number of reference memory errors compared with the stressed animals. Also, EE per se significantly increased the cell proliferation compared with controls. Furthermore, stress significantly reduced the hippocampal volume that was reversed after EE. Our observations demonstrate that short‐term EE completely ameliorates the stress‐induced decrease in cell proliferation and learning deficit, thus demonstrating the efficiency of rehabilitation in reversal of stress‐induced deficits and suggesting a probable role of newly formed cells in the effects of EE. © 2008 Wiley‐Liss, Inc.