Miracle-dz/UniFAR-FTUs huggingface dataset:
ADH1B Arg47His Polymorphism Is Associated with Esophageal Cancer Risk in High-Incidence Asian Population: Evidence from a Meta-Analysis

Background and Objectives Incidence of Esophageal squamous cell carcinoma (ESCC) is prevalent in Asian populations, especially in the ones from the “Asian esophageal cancer belt” along the Silk Road and the ones from East Asia (including Japan). Silk Road and Eastern Asia population genetics are relevant to the ancient population migration from central China. The Arg47His (rs1229984) polymorphism of ADH1B is the highest in East Asians, and ancient migrations along the Silk Road were thought to be contributive to a frequent ADH1B*47His allele in Central Asians. This polymorphism was identified as responsible for susceptibility in the first large-scale genome-wide association study of ESCC and that's explained by its modulation of alcohol oxidization capability. To investigate the association of ADH1B Arg47His with ESCC in Asian populations under a common ancestry scenario of the susceptibility loci, we combined all available studies into a meta-analysis. Methods A dataset composed of 4,220 cases and 8,946 controls from twelve studies of Asian populations was analyzed for ADH1B Arg47His association with ESCC and its interactions with alcohol drinking and ALDH2 Glu504Lys. Heterogeneity among studies and their publication bias were also tested. Results The ADH1B*47Arg allele was found to be associated to increased risk of ESCC, with the odds ratios (OR) being 1.62 (95% CI: 1.49–1.76) and 3.86 (2.96–5.03) for the His/Arg and the Arg/Arg genotypes, respectively. When compared with the His/His genotype of non-drinkers, the Arg/Arg genotype can interact with alcohol drinking and greatly increase the risk of ESCC (OR = 20.69, 95%CI: 5.09–84.13). Statistical tests also showed gene-gene interaction of ADH1B Arg+ with ALDH2 Lys+ can bring more risk to ESCC (OR = 13.46, 95% CI: 2.32–78.07). Conclusion Revealed by this meta-analysis, ADH1B*47Arg as a common ancestral allele can significantly increase the risk of ESCC in Asians, especially when coupled with alcohol drinking or the ALDH2*504Lys allele.
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson–Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.
An efficient reuse system for digital circuit design

In this paper a complete reuse system for digital circuit design is presented. Thereby 'design for reuse' and 'design by reuse' aspects are considered. In particular a repository for IPs with special emphasis on classification and selection, web integration and IP protection is developed. By practising intra-company reuse with our system the efficiency and performance of reuse is demonstrated.
A stereo vision measurement system Based on OpenCV

A complete realization method of stereo vision measurement system based on Open Source Computer Vision(OpenCV) was presented in this paper. Firstly, camera calibration based on 3D grid target was used to establish the relationship between the positions of the pixels and the scene points. This step was accomplished by OpenCV functions. Secondly, Harris corner detection was selected to get the feature points. Then, corresponding points between stereo images were calculated by sparse point matching algorithm. And epipolar constraint was added in the matching process in order to improve the accuracy and efficiency. Finally, 3D world coordinates of each feature pixel were derived from matching relationship and camera model. And then, the real size of the object was ascertained subsequently. Experimental results showed that the proposed method can build a complete and viable stereo vision measurement system.
Des-gamma-carboxy prothrombin as an important prognostic indicator in patients with small hepatocellular carcinoma.

AIM To clarify the effect of a high des-gamma-carboxy prothrombin (DCP) level on the invasiveness and prognosis of small hepatocellular carcinoma. METHODS Among 142 consecutive patients with known DCP levels, who underwent hepatectomy because of hepatocellular carcinoma, 85 patients met the criteria for small hepatocellular carcinoma, i.e. one<or=5 cm sized single tumor or no more than three<or=3 cm sized tumors. RESULTS The overall survival rate of the 142 patients was 92.1% for 1 year, 69.6% for 3 years, and 56.9% for 5 years. Multivariate analysis showed that microscopic vascular invasion (P=0.03) and serum DCP>or=400 mAU/mL (P=0.02) were independent prognostic factors. In the group of patients who met the criteria for small hepatocellular carcinoma, DCP>or=400 mAU/mL was found to be an independent prognostic factor for recurrence-free (P=0.02) and overall survival (P=0.0005). In patients who did not meet the criteria, the presence of vascular invasion was an independent factor for recurrence-free (P=0.02) and overall survivals (P=0.01). In 75% of patients with small hepatocellular carcinoma and high DCP levels, recurrence occurred extrahepatically. CONCLUSION For small hepatocellular carcinoma, a high preoperative DCP level appears indicative for tumor recurrence. Because many patients with a high preoperative DCP level develop extrahepatic recurrence, it is necessary to screen the whole body.
A Reduced Feedback Precoder for Cooperative Relay Networks

A new precoder that reduces the feedback overhead in an OFDM-based relay network is proposed. A joint Singular Value Decomposition (SVD) and QR Decomposition is employed at the source-destination link and source-relay-destination link. Using the proposed precoder, only one precoding matrix needs to be fed back, independent of the total number of subcarriers. The link achievable rate using the reduced complexity precoder is evaluated via simulations and compared with that of full SVD precoders and for varying codebook size.
Endoscopy-Assisted Percutaneous Repair of Acute Achilles Tendon Tears

Background: We developed a technique for endoscopy-assisted percutaneous repair of acute Achilles tendon tears. Methods: Nineteen patients with acute Achilles tendon tears were prospectively recruited into the study. All patients (18 male, 1 female) had sports-related injuries. Preoperative diagnosis was made from patient history, physical examination, and sonography. The average patient age was 38.7 years, and follow-up averaged 24 months. All patients received endoscopy-assisted percutaneous Achilles tendon repair with modified Bunnell sutures passed by bird beak and No. 5 Ethibond under direct visualization using 4.0-mm arthroscopy. Results were evaluated by physical examination, sonography, and magnetic resonance imaging (MRI). Results: All 19 patients achieved tendon healing. All patients were evaluated by sonography, and the tendons of 16 patients were imaged using MRI to evaluate the extent of healing. Final dorsiflexion was 16 degrees and plantar flexion 26 degrees, and 95% of the patients (18/19) returned to their previous level of sporting activity. One patient developed a superficial infection, and 2 patients had postoperative sural nerve injury with numbness for 1 month. There were no other major complications. Conclusion: Endoscopy-assisted percutaneous repair of the Achilles tendon allowed good tendon healing and return to sports at 6 months. Sural nerve injury during surgery was a potential complication of this procedure. Level of Evidence: Level IV, retrospective case series.
Molecular cloning and cell-specific growth characterization of polymorphic variants of type D serogroup 2 simian retroviruses.

Simian retroviruses (SRVs), the etiological agent of a spontaneous Simian acquired immunodeficiency syndrome, endemically infects large percentages of Asian macaques housed in biomedical research colonies and severely compromises the effective use of these species as a viable research animal. We recently described the molecular cloning of a serogroup 2 SRV, D2/RHE/OR, which causes mild immunosuppression in rhesus macaques. A restriction site variant, D2/RHE/OR/V1, has also been recovered from severely ill animals endemically infected with D2/RHE/OR. We now report the complete nucleotide sequences of D2/RHE/OR and D2/RHE/OR/V1. Both infectious molecular clones retain the genetic structure typical of type D SRVs (5' LTR-gag-prt-pol-env-3'LTR) and encode identically sized 8105-bp proviruses. D2/RHE/OR and D2/RHE/OR/V1 are 99.3% similar at the amino acid level, exhibiting only 17 residue differences, of which 10 are located in the envelope glycoproteins. The molecular clones and reciprocal chimeric viruses were used to assess the contribution of different genetic domains to virus infectivity in a T cell infection assay. These experiments indicate that D2/RHE/OR has a reduced ability to infect specific T cell lines, especially Hut-78 and MT-4 cells, and that the envelope gene is not the sole determinant of in vitro tropism.
Removing Guns From Batterers

Persons under certain domestic violence restraining orders in California are required to surrender any firearms in their possession within 24 hours of service. The California Department of Justice funded a pilot program in which Sheriff’s Offices in two counties developed a system for better enforcing the firearm surrender requirement. As part of a larger process evaluation, 17 restraining order recipients were interviewed about their experiences with and feelings about the removal of firearms from their abusers. Most women surveyed wanted firearms removed and felt safer as a result of their removal. Implications of the findings are discussed.
Conjugate strike‐slip faulting along the Bangong‐Nujiang suture zone accommodates coeval east‐west extension and north‐south shortening in the interior of the Tibetan Plateau

Geologic investigations of how the Tibetan plateau is currently deforming have focused primarily on its boundary faults. Consequently, how the interior of the plateau deforms remains poorly understood. To fill this gap in knowledge, we conducted field mapping, analysis of remote sensing and digital topographic data, and reinterpretation of existing geologic maps in central Tibet. This study reveals a 200–300 km wide and 1500–1800 km long east trending zone conjugate strike‐slip faults across central Tibet. The central Tibet conjugate fault zone is comprised of northeast striking left‐slip faults north of the Bangong‐Nujiang suture and northwest striking right‐slip faults south of the suture zone. These strike‐slip faults are kinematically linked with north trending Tibetan rifts located north and south of the conjugate fault systems. Without exception, all conjugate faults intersect or merge toward one another along the Bangong‐Nujiang suture zone. Motion on these faults accommodates coeval east‐west extension and north‐south contraction. To determine the fault kinematics and the magnitude of fault slip, we investigated three conjugate fault sets in the central Tibet fault zone. These include from east to west, the Dong Co, Bue Co, and Aishi Co conjugate fault systems, which are adjacent to the Bangong‐Nujiang suture zone and separated by a distance of 400 and 70 km, respectively. The average magnitude of fault motion on individual strike‐slip faults is ∼12 km as determined by offsets of Tertiary thrusts and Paleozoic‐Mesozoic lithologic units. The conjugate fault configuration requires ∼12 km of north‐south contraction across the 200–300 km fault zone since its initiation. Because the conjugate strike‐slip faults are kinematically linked with the north trending Tibetan rifts which initiated between 14 and 8 Ma, our estimated magnitude of north‐south contraction implies a contraction rate of ∼1–2 mm/yr across central Tibet. The relatively closely spaced (<150 km) basins may result from a series of conjugate strike‐slip fault systems in the interior of Tibet. These structures likely formed by eastward spreading of the Tibetan crust via distributed eastward extrusion of small (<150 km wide) wedge‐shaped crustal blocks that leave a space at their trailing end.
Prediction of onset and course of high hospital utilization in sickle cell disease.

BACKGROUND Although sickle cell disease (SCD) patients typically manage their pain at home, a small subgroup is frequently hospitalized and accounts for the majority of costs. OBJECTIVES 1) To identify prospective diagnostic and demographic markers of new periods of high utilization; 2) To identify demographic and diagnostic markers of a persistent rather than moderating course of high utilization; 3) To replicate the finding that high utilization tends to moderate. DESIGN The State Inpatient Databases for California, 2004-2007, were used. Patients with new onset periods of high utilization were compared with non-high utilizers, and new high utilizers who moderated were compared with those who had a persistent course. SETTING All hospitals in the state of California. PATIENTS Patients age 13 years or older in 2004 with a recorded diagnosis of sickle cell disease and at least one hospitalization for crisis during the study period. MEASURES METHODS Groups from hospitals throughout California were compared on demographics and discharge diagnoses of SCD complications and comorbidities. Patients age 13 years or older in 2004 with a recorded diagnosis of sickle cell disease and at least 1 hospitalization for crisis during the study period were included. RESULTS New periods of high utilization were associated with more prior hospitalizations and previous diagnoses of aseptic necrosis and renal disease. High utilization typically moderated. A persistent course was associated with slightly more hospitalizations during the initial year of high utilization, and, subsequently, by more mentions of septicemia and mood disorders. CONCLUSIONS Overall, high utilization was difficult to predict, as was its course. The diagnoses most associated with high utilization indicated more severe sickle cell disease. Septicemia deserves further investigation as a preventable cause for high utilization, as do mood disorders.
The Totem system

The Totem system supports fault-tolerant applications in which distributed processes cooperate to perform a common task and in which replicated data must be updated consistently in the presence of asynchrony and faults. Reliable totally ordered delivery of messages to processes within process groups is provided on a single local-area network or over multiple local-area networks interconnected by gateways. Message ordering is consistent across the entire network, despite processor and communication faults, without requiring all processes to deliver all messages. The Totem system handles processor failure and recovery, as well as network partitioning and remerging, and provides membership and topology maintenance services. <<ETX>>
Molecular regulations governing TREK and TRAAK channel functions

K+ channels with two-pore domain (K2p) form a large family of hyperpolarizing channels. They produce background currents that oppose membrane depolarization and cell excitability. They are involved in cellular mechanisms of apoptosis, vasodilatation, anesthesia, pain, neuroprotection and depression. This review focuses on TREK-1, TREK-2 and TRAAK channels subfamily and on the mechanisms that contribute to their molecular heterogeneity and functional regulations. Their molecular diversity is determined not only by the number of genes but also by alternative splicing and alternative initiation of translation. These channels are sensitive to a wide array of biophysical parameters that affect their activity such as unsaturated fatty acids, intra- and extracellular pH, membrane stretch, temperature, and intracellular signaling pathways. They interact with partner proteins that influence their activity and their plasma membrane expression. Molecular heterogeneity, regulatory mechanisms and protein partners are all expected to contribute to cell specific functions of TREK currents in many tissues.
Locomotion generator for robotic fish using an evolutionary optimized central pattern generator

Central Pattern Generator (CPG) consists of biological neural networks that generate coordinated rhythmic signals for the control of locomotion of vertebrate and invertebrate animals, such as walking, running, swimming and flying. In this paper, an evolutionary optimized CPG structure is proposed for generating fish-like locomotion of the robotic fish by controlling the flapping angles of all joints. The proposed CPG structure consists of three neural oscillators and each neural oscillator generates rhythmic signals for the corresponding joint of the three-joint robotic fish. The CPG structure for autonomous repeated locomotion has the parameters which determine the form of output signals. Quantum-inspired Evolutionary Algorithm (QEA) is employed for optimizing these parameters to generate signals which track the kinematically derived fish-like locomotion. The effectiveness of the proposed CPG structure is demonstrated by computer simulations.
Performance of cage-less interior PM motor with open-loop inverter drive

The performance of a cage-less 16-kW, 1,500-rpm interior permanent magnet machine developed for a portable generator application is examined when run as a motor under open-loop volts-per-hertz control from an inverter. The analytical and experimental steady-state results show the machine can operate with high power-factor and efficiency. The dynamic results show robust operation in starting and the capability to maintain synchronism even with large step load transients. The motor performance is promising for applications requiring high efficiency, particularly where variable-speed operation is needed or where multiple motors can be run from the same inverter.
Response Fingerprinting: a probabilistic method for evaluating the network response to stimuli

Spiking neural networks that have variable connection delays have the interesting property that they are sensitive to both spatial and temporal patterns of input. Each neuron in the network receives input from spatially-distributed input neurons whose precise ﬁring times interact with connection delays to determine whether the neuron can exceed the ﬁring threshold and produce an output. The network is therefore most responsive to spatio-temporal stimuli whose temporal components match the delays in the connected structure of the network. Izhikevich (2006a) has shown that certain strongly connected groups of neurons known as polychronous neural groups (or PNGs) exist in large numbers within the network structure. The activation of these neural groups is stimulus-speciﬁc and produces unique ﬁring signatures that are detectable in the ﬁring data. Previous methods for detecting PNG activation have relied on a template matching technique that assumes a deterministic response to each stimulus presentation (Izhikevich, 2006a; Martinez and Paugam-Moisy, 2009; Guise et al., 2013a). Here we present an alternative probabilistic view of the stimulus response and demonstrate the application of this new detection method.
Inadequate reporting of research ethics review and informed consent in cluster randomised trials: review of random sample of published trials

Objectives To investigate the extent to which authors of cluster randomised trials adhered to two basic requirements of the World Medical Association’s Declaration of Helsinki and the International Committee of Medical Journal Editors’ uniform requirements for manuscripts (namely, reporting of research ethics review and informed consent), to determine whether the adequacy of reporting has improved over time, and to identify characteristics of cluster randomised trials associated with reporting of ethics practices. Design Review of a random sample of published cluster randomised trials from an electronic search in Medline. Setting Cluster randomised trials in health research published in English language journals from 2000 to 2008. Study sample 300 cluster randomised trials published in 150 journals. Results 77 (26%, 95% confidence interval 21% to 31%) trials failed to report ethics review. The proportion reporting ethics review increased significantly over time (P<0.001). Trials with data collection interventions at the individual level were more likely to report ethics review than were trials that used routine data sources only (79% (n=151) v 55% (23); P=0.008). Trials that accounted for clustering in the design and analysis were more likely to report ethics review. The median impact factor of the journal of publication was higher for trials that reported ethics review (3.4 v 2.3; P<0.001). 93 (31%, 26% to 36%) trials failed to report consent. Reporting of consent increased significantly over time (P<0.001). Trials with interventions targeting participants at the individual level were more likely to report consent than were trials with interventions targeting the cluster level (87% (90) v 48% (41); P<0.001). Trials with data collection interventions at the individual level were more likely to report consent than were those that used routine data sources only (78% (146) v 29% (11); P<0.001). Conclusions Reporting of research ethics protections in cluster randomised trials is inadequate. In addition to research ethics approval, authors should report whether informed consent was sought, from whom consent was sought, and what consent was for.
Radiation-induced double-strand breaks require ATM but not Artemis for homologous recombination during S-phase

Double-strand breaks (DSBs) are repaired by two distinct pathways, non-homologous end joining (NHEJ) and homologous recombination (HR). The endonuclease Artemis and the PIK kinase Ataxia-Telangiectasia Mutated (ATM), mutated in prominent human radiosensitivity syndromes, are essential for repairing a subset of DSBs via NHEJ in G1 and HR in G2. Both proteins have been implicated in DNA end resection, a mandatory step preceding homology search and strand pairing in HR. Here, we show that during S-phase Artemis but not ATM is dispensable for HR of radiation-induced DSBs. In replicating AT cells, numerous Rad51 foci form gradually, indicating a Rad51 recruitment process that is independent of ATM-mediated end resection. Those DSBs decorated with Rad51 persisted through S- and G2-phase indicating incomplete HR resulting in unrepaired DSBs and a pronounced G2 arrest. We demonstrate that in AT cells loading of Rad51 depends on functional ATR/Chk1. The ATR-dependent checkpoint response is most likely activated when the replication fork encounters radiation-induced single-strand breaks leading to generation of long stretches of single-stranded DNA. Together, these results provide new insight into the role of ATM for initiation and completion of HR during S- and G2-phase. The DSB repair defect during S-phase significantly contributes to the radiosensitivity of AT cells.