Miracle-dz/UniFAR-FTUs huggingface dataset:
Unified Deep Learning Architecture for Modeling Biology Sequence

Prediction of the spatial structure or function of biological macromolecules based on their sequences remains an important challenge in bioinformatics. When modeling biological sequences using traditional sequencing models, long-range interaction, complicated and variable output of labeled structures, and variable length of biological sequences usually lead to different solutions on a case-by-case basis. This study proposed a unified deep learning architecture based on long short-term memory or a gated recurrent unit to capture long-range interactions. The architecture designs the optional reshape operator to adapt to the diversity of the output labels and implements a training algorithm to support the training of sequence models capable of processing variable-length sequences. The merging and pooling operators enhances the ability of capturing short-range interactions between basic units of biological sequences. The proposed deep-learning architecture and its training algorithm might be capable of solving currently variable biological sequence-modeling problems under a unified framework. We validated the model on one of the most difficult biological sequence-modeling problems, protein residue interaction prediction. The results indicate that the accuracy of obtaining the residue interactions of the model exceeded popular approaches by 10 percent on multiple widely-used benchmarks.
Biological activities of ophiobolin K and 6-epi-ophiobolin K produced by the endophytic fungus Aspergillus calidoustus

Endophytic fungi represent ubiquitous microbial organisms able to live in the tissues of different plants around the world and represent a prolific source of bioactive metabolites. In the present study, the endophytic fungus Aspergillus calidoustus was isolated from the medicinal plant Acanthospermum australe (Asteraceae), and identified using molecular, physiological and morphological methods. A methylene chloride crude extract of A. calidoustus has been produced and subjected to antifungal bioassay-directed fractionation which resulted in the isolation of the two bioactive compounds: ophiobolin K and 6-epi-ophiobolin K. These pure compounds displayed antifungal activity against fungal plant pathogens, protozoal activity against Trypanosoma cruzi, and cytotoxic activity against human tumoral cell lines. The results show that A. calidoustus was able to produce the antifungal and cytotoxic metabolites ophiobolin K and 6-epi-ophiobolin K, which may help the fungus to colonise and occupy the substratum as well as survive in natural environments.
Computer aided design and analysis of piston mechanism of four stroke S.I. engine

This paper illustrates design procedure, kinematics and dynamic analysis of piston of single cylinder of air-cooling S.I. engine at maximum power and maximum torque condition. It is the study of the geometry of motion. Kinematics analysis involves determination of position, displacement, rotation speed, velocity and acceleration and inertia force and dynamic analysis involves determination of tangential force, radial force, forces on bearing, and torque on the crankshaft. In this paper the complete kinematic and combined static and dynamic force analysis of a single cylinder, four stroke internal combustion engines are discussed. The Complex Algebra analytical approach is used for analysis is less time consuming if it is programmed for the computer solution. The pressure for one cycle at maximum power condition data for the analysis of the engine has been calculated by using Engine Pro V 3.9 engine cycle simulation program software. The computer program is prepared in visual basic language software for Kinematic and dynamic analysis of the engine at the every crank interval.
Levofloxacin-Resistant Invasive Streptococcus pneumoniae in the United States: Evidence for Clonal Spread and the Impact of Conjugate Pneumococcal Vaccine

ABSTRACT The emergence of fluoroquinolone resistance in sterile-site isolates of Streptococcus pneumoniae is documented in this study characterizing all invasive levofloxacin-resistant (MIC, ≥8 mg/liter) S. pneumoniae isolates (n = 50) obtained from the Centers for Disease Control and Prevention Active Bacterial Core Surveillance from 1998 to 2002. Resistance among all isolates increased from 0.1% in 1998 to 0.6% in 2001 (P = 0.008) but decreased to 0.4% in 2002, while resistance among vaccine serotypes continued to increase from 0.3% in 1998 to 1.0% in 2002, suggesting that fluoroquinolones continue to exert selective pressure on these vaccine serotypes. Only 22% of resistant isolates were not covered by the conjugate vaccine serogroups. Multilocus sequence typing revealed that 58% of resistant strains were related to five international clones identified by the Pneumococcal Molecular Epidemiology Network, with the Spain23F-1 clone being most frequent (16% of all isolates). Thirty-six percent of the isolates were coresistant to penicillin, 44% were coresistant to macrolides, and 28% were multiresistant to penicillin, macrolides, and fluoroquinolones. Fifty percent of the isolates were resistant to any three drug classes. Ninety-four percent of the isolates had multiple mutations in the quinolone resistance-determining regions of the gyrA, gyrB, parC, and parE genes. In 16% of the isolates, there was evidence of an active efflux mechanism. An unusual isolate was found that showed only a single parE mutation and for which the ciprofloxacin MIC was lower (2 mg/liter) than that of levofloxacin (8 mg/liter). Our results suggest that invasive pneumococcal isolates resistant to levofloxacin in the United States show considerable evidence of multiple resistance and of clonal spread.
Algorithm based on multiple filters for elephant flows identification

Identifying elephant flows is very important in developing effective and efficient traffic engineering schemes. In this paper, according to the characteristic of network flows, an algorithm based on multiple filters is proposed to realize elephant flows identification. Multiple filters algorithm improves the performance and saves the storage from three aspects: large flows handled firstly, using Timeout-Counting Bloom Filter to filtrate small flows and using Multilayer Counting Bloom Filters to identify large flows. The theoretical analysis and the simulation result indicates that under the condition of existing some tolerable measurement error about the length of flows, our algorithm can identify elephant flows accurately, which reduce the storage space and improve the processing speed efficiently.
Control strategy for a single phase bidirectional converter based UPS system using FPGA

Uninterruptible power supplies are widely used to supply uninterrupted power to the loads under power failure. Typical UPS systems consists of two power converters namely a rectifier/charger which charges the batteries and an inverter to provide an ac sinusoidal output. Employing a single converter for both rectification and inversion process reduces the hardware components. This paper presents a control strategy for the single phase bidirectional converter used in UPS systems. Under normal mode, the grid supplies the loads and charges the battery through the bidirectional converter. The converter is controlled using a hysteresis current controller and a constant current charging technique is used to charge the batteries. Upon grid failure, the battery supplies the load through the converter which operates in voltage control mode to maintain the load voltage. This system offers the advantage of reduced hardware, low harmonic distortion of line current and regulation of load voltage under grid failure. The control strategy is simulated in MATLAB/Simulink and implemented in an ALTERA cyclone II FPGA board. The steady state and the dynamic response of the system are simulated and verified experimentally on the prototype unit built in the laboratory.
Referral bias in hospital register studies of geographical and industrial differences in health.

INTRODUCTION The Danish National Hospital Register contains four patient types: full-time inpatients, part-time inpatients, outpatients and emergency ward patients. The aim of the present study was to investigate whether results from comparative hospital register studies depend on which patient types we choose to include in the analysis. METHODOLOGY The hospital register was linked to the centralised civil register and the employment classification module. All economically active persons in Denmark aged 20-59 years 1st January 1995 (N = 2,281,480) were followed for six years. We calculated SIRs, first by county then by industry and finally by industry adjusted for county, for a variety of diagnostic groups and for each of the following types of cases: A) full-time inpatients, B) all inpatients, C) all inpatients and outpatients, D) all patients. The ratio between the maximum and the minimum of the four types of SIRs was calculated for each combination of the examined population groups and diseases. A max/min ratio was regarded as a sign of referral bias if it was above 1.2 and statistically significant. RESULTS When calculating SIRs by county 46.7 percent of the max/min ratios signified referral bias. The percentage was 5.5 when calculating SIRs by industry and only 1.7 when they were calculated by industry adjusted for county. CONCLUSIONS Estimates of geographical health differences are often distorted by differences in the health care organisation. Estimates of industrial health differences tend to be robust with a few identifiable exceptions. Standardisation for county will eliminate bias.
Lenalidomide and dexamethasone in transplant-ineligible patients with myeloma.

BACKGROUND The combination melphalan-prednisone-thalidomide (MPT) is considered a standard therapy for patients with myeloma who are ineligible for stem-cell transplantation. However, emerging data on the use of lenalidomide and low-dose dexamethasone warrant a prospective comparison of the two approaches. METHODS We randomly assigned 1623 patients to lenalidomide and dexamethasone in 28-day cycles until disease progression (535 patients), to the same combination for 72 weeks (18 cycles; 541 patients), or to MPT for 72 weeks (547 patients). The primary end point was progression-free survival with continuous lenalidomide-dexamethasone versus MPT. RESULTS The median progression-free survival was 25.5 months with continuous lenalidomide-dexamethasone, 20.7 months with 18 cycles of lenalidomide-dexamethasone, and 21.2 months with MPT (hazard ratio for the risk of progression or death, 0.72 for continuous lenalidomide-dexamethasone vs. MPT and 0.70 for continuous lenalidomide-dexamethasone vs. 18 cycles of lenalidomide-dexamethasone; P<0.001 for both comparisons). Continuous lenalidomide-dexamethasone was superior to MPT for all secondary efficacy end points, including overall survival (at the interim analysis). Overall survival at 4 years was 59% with continuous lenalidomide-dexamethasone, 56% with 18 cycles of lenalidomide-dexamethasone, and 51% with MPT. Grade 3 or 4 adverse events were somewhat less frequent with continuous lenalidomide-dexamethasone than with MPT (70% vs. 78%). As compared with MPT, continuous lenalidomide-dexamethasone was associated with fewer hematologic and neurologic toxic events, a moderate increase in infections, and fewer second primary hematologic cancers. CONCLUSIONS As compared with MPT, continuous lenalidomide-dexamethasone given until disease progression was associated with a significant improvement in progression-free survival, with an overall survival benefit at the interim analysis, among patients with newly diagnosed multiple myeloma who were ineligible for stem-cell transplantation. (Funded by Intergroupe, Francophone du Myélome and Celgene; FIRST ClinicalTrials.gov number, NCT00689936; European Union Drug Regulating Authorities Clinical Trials number, 2007-004823-39.).
A high‐performance polycarbonate electrophoresis microchip with integrated three‐electrode system for end‐channel amperometric detection

A fully integrated polycarbonate (PC) microchip for CE with end‐channel electrochemical detection operated in an amperometric mode (CE‐ED) has been developed. The on‐chip integrated three‐electrode system consisted of a gold working electrode, an Ag/AgCl reference electrode and a platinum counter electrode, which was fabricated by photo‐directed electroless plating combined with electroplating. The working electrode was positioned against the separation channel exit to reduce post‐channel band broadening. The electrophoresis high‐voltage (HV) interference with the amperometric detection was assessed with respect to detection noise and potential shifts at various working‐to‐reference electrode spacing. It was observed that the electrophoresis HV interference caused by positioning the working electrode against the channel exit could be diminished by using an on‐chip integrated reference electrode that was positioned in close proximity (100 μm) to the working electrode. The CE‐ED microchip was demonstrated for the separation of model analytes, including dopamine (DA) and catechol (CA). Detection limits of 132 and 164 nM were achieved for DA and CA, respectively, and a theoretical plate number of 2.5×104/m was obtained for DA. Relative standard deviations in peak heights observed for five runs of a standard solution containing the two analytes (0.1 mM for each) were 1.2 and 3.1% for DA and CA, respectively. The chip could be continuously used for more than 8 h without significant deterioration in analytical performance.
Antiviral drug resistance in herpesviruses other than cytomegalovirus

The discovery of acyclovir (ACV), a nucleoside analogue, more than 30 years ago, represents a milestone in the management of HSV and VZV infections. The modest activity of ACV against CMV prompted the development of another nucleoside analogue, ganciclovir, for the management of systemic and organ‐specific CMV diseases. Second‐line agents such as the pyrophosphate analogue foscarnet and the nucleotide analogue cidofovir have been approved subsequently. In contrast to ACV and ganciclovir, the latter drugs do not require selective phosphorylation by viral protein kinases to be converted into their active forms. Since the introduction of these antivirals, the emergence of drug‐resistant mutants has been constantly reported particularly in severely immunocompromised patients such as bone marrow and solid organ transplant recipients as well as HIV‐infected individuals. In this manuscript, we discuss the characteristics of the antiviral agents currently approved for the management of HSV, VZV and CMV diseases. In recent years, the resistance of CMV to antiviral drugs has been extensively reviewed. The emergence of antiviral drug resistance is also observed with other members of the Herpesviridae family, namely HSV‐1, HSV‐2, VZV and HHV‐6, which are the focus of this review. More specifically, we describe the laboratory methods for assessing drug susceptibilities, the frequency and clinical significance of drug‐resistant infections and their management. Copyright © 2014 John Wiley & Sons, Ltd.
Mast-cell infiltration of airway smooth muscle in asthma.

BACKGROUND Asthma and eosinophilic bronchitis are characterized by similar inflammatory infiltrates in the submucosa of the lower airway. However, eosinophilic bronchitis differs from asthma in that there is no variable airflow obstruction or airway hyperresponsiveness in the former condition. We tested the hypothesis that there were differences between the two conditions in the microlocalization of mast cells within the airway smooth muscle. METHODS Immunohistochemical analysis of bronchial-biopsy specimens was completed in 17 subjects with asthma, 13 subjects with eosinophilic bronchitis, and 11 normal controls recruited from two centers. RESULTS Both groups with disease had a similar degree of submucosal eosinophilia and thickening of the basement membrane and lamina reticularis. By contrast, the number of tryptase-positive mast cells in the bundles of airway smooth muscle from subjects with asthma (median, 5.1 mast cells per square millimeter of smooth muscle [range, 0 to 33.3]) was substantially higher than that in subjects with eosinophilic bronchitis (median, 0 mast cells per square millimeter; range, 0 to 4.8) and that in normal controls (median, 0 mast cells per square millimeter [range, 0 to 6.4]; P<0.001 for the comparison among the three groups). T cells and eosinophils were not usually seen in the airway smooth muscle in any of the groups. CONCLUSIONS The infiltration of airway smooth muscle by mast cells is associated with the disordered airway function found in asthma.
Snake view: exploring thermal imaging as a vision extender in mountains

Human's vision can only operate in the limited visible band of the electromagnetic spectrum. Using commercially available imaging sensors can be beneficial to extend human's visual perception in different environments. Typically, these environments include challenging conditions, for instance smoky views during a fire or occluded, foggy, cloudy and windy view in mountain environments. Recently, thermal imaging became more commercially available, which makes utilizing it to extend the human's visual perception affordable and deployable. In this paper, we propose the usage of thermal imaging as a vision extension tool. Two initial prototypes are presented depicting the different form factors of thermal cameras attachment to Head Mounted Displays. Finally, we discuss potential use case of extending the human's vision to cover the thermal spectrum during mountains activities.
Cutting Edge: A Novel Toll/IL-1 Receptor Domain-Containing Adapter That Preferentially Activates the IFN-β Promoter in the Toll-Like Receptor Signaling1

MyD88 is a Toll/IL-1 receptor (TIR) domain-containing adapter common to signaling pathways via Toll-like receptor (TLR) family. However, accumulating evidence demonstrates the existence of a MyD88-independent pathway, which may explain unique biological responses of individual TLRs, particularly TLR3 and TLR4. TIR domain-containing adapter protein (TIRAP)/MyD88 adapter-like, a second adapter harboring the TIR domain, is essential for MyD88-dependent TLR2 and TLR4 signaling pathways, but not for MyD88-independent pathways. Here, we identified a novel TIR domain-containing molecule, named TIR domain-containing adapter inducing IFN-β (TRIF). As is the case in MyD88 and TIRAP, overexpression of TRIF activated the NF-κB-dependent promoter. A dominant-negative form of TRIF inhibited TLR2-, TLR4-, and TLR7-dependent NF-κB activation. Furthermore, TRIF, but neither MyD88 nor TIRAP, activated the IFN-β promoter. Dominant-negative TRIF inhibited TLR3-dependent activation of both the NF-κB-dependent and IFN-β promoters. TRIF associated with TLR3 and IFN regulatory factor 3. These findings suggest that TRIF is involved in the TLR signaling, particularly in the MyD88-independent pathway.
Genomewide linkage scan in a multigeneration Caucasian pedigree identifies a novel locus for keratoconus on chromosome 5q14.3-q21.1

Purpose: Keratoconus is a corneal dystrophy with an incidence of 1 in 2000 and a leading cause for cornea transplantation in Western developed countries. Both clinical observations and segregation analyses suggest a major role for genes in its pathogenesis. It is genetically heterogenous, most commonly sporadic, but inherited patterns with recessive or dominant modes have also been reported. We studied a four-generation autosomal-dominant pedigree to identify disease loci for keratoconus.Methods: A two-stage genome-wide scan was applied to 27 family members. First linkage analysis was performed with 343 microsatellite markers along the 22 autosomal chromosomes at ≈10 cM density. This was followed by fine mapping at ≈2 cM density, in regions suggestive of linkage. Multipoint linkage analysis was performed using GeneHunter2.Results: Evidence of suggestive linkage from the initial scan was observed at the 82 to 112 cM region of chromosome 5q14.1-q21.3 with a maximum lod score (LOD) of 3.48 (penetrance = 0.5). Fine mapping by testing an additional 11 microsatellite markers at 1 to 3 cM intervals revealed a narrower and higher peak (99–119 cM) with LOD 3.53. By analysis of the recombination of haplotypes, the putative locus of keratoconus was further narrowed to a 6 cM region (8.2 Mbp physical distance) between markers D5S2499 and D5S495.Conclusion: These results indicate a promising new locus for keratoconus in this pedigree. Because of the heterogeneous nature of keratoconus, this locus may be specific to familial autosomal-dominant keratoconus. Nevertheless, the identification of this locus may provide new insights into the pathogenesis of keratoconus.
The cross-cultural variation of predictors of human papillomavirus vaccination intentions.

BACKGROUND The influence of health beliefs on human papillomavirus (HPV) vaccine acceptability have been extensively documented in past research. However, studies documenting the generalizability of prior findings to culturally diverse participants are lacking. The importance of generalizability studies is underscored by the immense disparities in cervical cancer rates across ethnicities. Moreover, theory in cultural psychology suggests that beliefs derived from personal expectations may not be the strongest predictors of intentions in individuals socialized in collectivist cultures. The purpose of this research was to investigate the strongest predictors of mothers' intentions to vaccinate their daughters across three cultural groups: Hispanic, non-Hispanic white, and African American. METHODS One hundred fifty mothers were recruited from Public Health Department clinics in Milwaukee, Wisconsin. Mothers were asked to answer measures that assessed personal and normative predictors of intentions. RESULTS Results indicated that predictors of vaccination intentions varied cross-culturally. Specifically, culture moderated the influence of norms on intentions. CONCLUSIONS Interventions designed for Hispanics may be more effective if norms, rather than attitudes, are targeted.
Design and implementation of a real-time network-based substation simulation system

This paper describes the architecture and the composition of a network-based substation simulation system. The concept of virtual simulation context is introduced and implemented for remote control among heterogeneous computer platforms. RTP/RTCP and dynamic QoS control mechanisms are used in the system to accomplish satisfied QoS. The experiments show that the system runs well both in LAN and in the Internet.