gebhart/patrepeval huggingface dataset:
ClassiPhages 2.0: Sequence-based classification of phages using Artificial Neural Networks (2019)

Abstract Background/ Motivation In the era of affordable next generation sequencing technologies we are facing an exploding amount of new phage genome sequences. This requests high throughput phage classification tools that meet the standards of the International Committee on Taxonomy of Viruses (ICTV). However, an accurate prediction of phage taxonomic classification derived from phage sequences still poses a challenge due to the lack of performant taxonomic markers. Since machine learning methods have proved to be efficient for the classification of biological data we investigated how artificial neural networks perform on the task of phage taxonomy. Results In this work, 5,920 constructed and refined profile Hidden Markov Models (HMMs), derived from 8,721 phage sequences classified into 12 well known phage families, were used to scan phage proteome datasets. The resulting Phage Family-proteome to Phage-derived-HMMs scoring matrix was used to develop and train an Artificial Neural Network (ANN) to find patterns for phage classification into one of the phage families. Results show that using the 100 fold cross-validation test, the proposed method achieved an overall accuracy of 84.18 %. The ANN was tested on a set of unclassified phages and resulted in a taxonomic prediction. The ANN prediction was benchmarked against the prediction resulting of multi-HMM hits, and showed that the ANN performance is dependent on the quality of the input matrix. Conclusions We believe that, as long as some phage families on public databases are underrepresented, multi-HMM hits can be used as a classification method to populate those phage families, which in turn will improve the performance and accuracy of the ANN. We believe that the proposed method is an effective and promising method for phage classification. The good performance of the ANN and HMM based predictor indicates the efficiency of the method for phage classification, where we foresee its improvement with an increasing number of sequenced viral genomes.
An anatomic study on the mechanism of shoulder medial rotation contracture in obstetrical brachial plexus palsy (2001)

Objective To observe the origin of the nerves innervating the subscapularis muscle and its anagonistic muscles at brachial plexus root or trunk level, and the blood supply of the subscapularis muscle in order to clarify the mechanism of subscapularis muscle contracture in obstetric brachial plexus palsy (OBPP). Methods 32 sides of adult human cadavers were used. The innervating nerve of the subscapularis muscle and its antagonistic muscles (the infraspinatus muscle, the teres minor muscle, the deltoid muscle and the supraspinatus muscle) were dissected retrogradely to trace its origin at the root and trunk level of the brachial plexus. The nerve fiber external diameter in the corresponding root and/or trunk was measured and the constituent ratios in the root and/or trunk of the brachial plexus were calculated. The nutrient arteries of the subscapularis muscle were observed to compare the number and distribution of the arteries to the upper parts of the subscapularis muscle and the lower parts. Results The nerve fibers innervating the subscapularis muscle mainly originated from the upper and middle trunk. The percentage in the upper trunk was (81.61 ± 6.85)%, while that in the middle trunk was (18.39 ± 6.85)%. The nerve fibers of its antagonistic muscles only originated from the upper trunk. Not only the number but also the diameter of the arteries entering the upper parts of the muscle was larger than those entering the lower parts. Conclusions The difference in the nerve fiber origin between the subscapularis muscle and its antagonistic muscles and the characteristics of the blood supply of the subscapularis muscle were the major causes of subscapularis muscle contracture in obstetric brachial plexus palsy.
Genetically modified keratinocytes transplanted to wounds reconstitute the epidermis. (1994)

Normal and retrovirally transfected keratinocyte suspensions expressing either the beta-galactosidase gene or the human growth hormone (hGH) gene were transplanted into chamber-enclosed skin full-thickness wounds of Yorkshire pigs. Immunostaining of sequential skin biopsies obtained for 4 weeks after transplantation showed survival of the transplanted keratinocytes as well as expression of beta-galactosidase. Transfected keratinocytes were first seen in the neodermal portions of the wounds, then in the regenerating basal epidermal layer, and finally in the terminally differentiating cells of the stratum spinosum. When keratinocytes transfected with the hGH gene were transplanted into similar wounds, hGH was detected for 10 days in wound fluid. In contrast, hGH was detected in vitro for 47 days. Wounds transplanted with either transfected or normal keratinocytes restored the epithelial barrier function significantly faster than nontransplanted controls (P < 0.05). The study confirms the successful transplantation of keratinocyte suspensions, their reconstitution of the epidermis, and their acceleration of repair. Further, this apparently normal incorporation of genetically engineered transplanted keratinocytes expressing either beta-galactosidase or hGH suggests the possibility of introducing other genes expressing therapeutic proteins into wounds to favorably affect healing. Wound fluid detection of the expressed peptide provided early demonstration of successful transfer of the hGH gene.
High-precision Si-micromachined micromirrors with on-chip actuation for external-cavity semiconductor lasers (1995)

External-cavity semiconductor lasers are of interest for applications such as laser-linewidth narrowing, emission wavelength tuning, and laser mode locking. One drawback of existing external-cavity lasers is the difficulty in maintaining mechanical stability for critical alignment of the bulk optical elements. Meanwhile, schemes schemes employing optical fibers as the external cavities offer no flexibility in varying the cavity length once the device is built. We demonstrate a silicon-micromachined on-chip actuated micromirror that can be used to construct robust, yet adjustable, external-cavity laser systems.
Improving logging and recovery performance in Phoenix/App (2004)

Phoenix/App supports software components whose states are made persistent across a system crash via redo recovery, replaying logged interactions. Our initial prototype force logged all request/reply events resulting from intercomponent method calls and returns. We describe an enhanced prototype that implements: (i) log optimizations to improve normal execution performance; and (ii) checkpointing to improve recovery performance. Logging is reduced in two ways: (1) we only log information required to remove nondeterminism, and we only force the log when an event "commits" the state of the component to other parts of the system; (2) we introduce new component types that provide our enhanced system with more information, enabling further reduction in logging. To improve recovery performance, we save the values of the fields of a component to the log in an application "checkpoint". We describe the system elements that we exploit for these optimizations, and characterize the performance gains that result.
Polyomavirus BK non‐coding control region rearrangements in health and disease (2007)

NCCR rearrangements are neither required nor a sufficient condition to produce clinical disease. BKV nephropathy and hemorrhagic cystitis are not associated with any unique NCCR configuration or nucleotide sequence.
A Bi-directional Interface linking a Dialysis Network with a Clinical Information Network (2009)

A clinical information system called OACIS is used in the Renal units of major hospitals of South Australia, integrating both patient dialysis and pathology data for clinical assessment. Fresenius haemodialysis machines have been installed in the majority of these Renal units and can be networked by the Finesse Basic system with collection of all patient treatment data into a local database (FinDB). In an effort to help care givers by minimizing data entry and reducing transcription errors, a bi-directional interface (FOXHL7) has been developed linking OACIS with FinDB. FOXHL7 provides automatic transfer of patient treatment data from FinDB to OACIS while allowing dialysis treatment orders to be exported from OACIS to Finesse prescriptions in FinDB. Data automatically uploaded to OACIS includes the patient's pre and post treatment weights, blood pressure measurements and other dialysis treatment information. Care providers can create new dialysis orders on any OACIS computer workstation with this information being downloaded into FinDB prescriptions at the appropriate dialysis centre. FOXHL7 is written in Microsoft Visual Basic and uses TCP Client/Server Active X technology to exchange HL7 Protocol messages with the OACIS Gateway engine. Transfer of the data occurs in real time as the dialysis treatment data becomes available in the Finesse database. The gateway processes the messages and new treatments are stored in OACIS. Changes to dialysis orders in OACIS are intercepted and broadcast to FOXHL7 for downloading to corresponding prescriptions in FinDB in real time. FOXHL7 resides on a Finesse Server running continuously seven days a week.
Determination of the Operational Environment of the Propeller Blades on Beech 1900D Aircraft (2008)

&lt;div class="htmlview paragraph"&gt;Data obtained from digital flight data recorders are used to assess the actual operational environment of propellers on a fleet of Beech 1900D aircraft in commuter role. Information is given on various aerodynamic parameters as well as those pertaining to engine and propeller usage. The takeoff rotation has been identified as the most demanding phase of flight in terms of unsteady loads exerted on the propeller blades. Special attention is paid to ground operations.&lt;/div&gt;
Family History of Colorectal Cancer in BRAF p.V600E-Mutated Colorectal Cancer Cases (2013)

These findings provide useful insights for cancer risk assessment in families and suggest that familial or inherited factors are more important in early-onset, BRAF-wild-type CRC.
Recombinant Rat and Mouse Growth Hormones: Risk Assessment of Carcinogenic Potential in 2-Year Bioassays in Rats and Mice (2007)

Recombinant rat growth hormone (rrGH) and recombinant mouse growth hormone (rmGH) were developed to evaluate the potential carcinogenicity of each biologically active growth hormone (GH) as assessed in the respective species. Biological activities of rrGH and rmGH were demonstrated by showing an increase in body weight gain and serum levels of insulin-like growth factor-1 (IGF-1) in hypophysectomized rats receiving daily sc injections for 6 days. With the exception of pharmacologically mediated weight gain, rrGH and rmGH had no adverse effects in 5-week oral toxicity studies and no production of anti-recombinant GH antibodies. The high doses selected for the carcinogenicity studies provided systemic exposures of GH up to approximately 10-fold over basal levels. In the 105-week mouse carcinogenicity study, daily sc injections of rmGH at 0.1, 0.2, or 0.5 mg/kg/day were well tolerated and had no effects on survival or incidence of tumors. In the 106-week rat carcinogenicity study, daily sc injections of rrGH at 0.2, 0.4, or 0.8 mg/kg/day had a favorable effect on longevity in female rats administered 0.4 or 0.8 mg/kg/day, an increased weight gain in females and males, and no increase in the incidence of tumors. The absence of carcinogenic effects of recombinant GH administered daily for 2 years to rodents was consistent with publications of clinical experience, indicating a lack of convincing evidence for an increased risk of cancer in children receiving human recombinant GH replacement therapy.
Gaming Away Stress: Using Biofeedback Games to Learn Paced Breathing (2018)

Biofeedback games are an attractive alternative to standard techniques for learning short-term relaxation skills. In this paper, we present the design, implementation, and evaluation of three respiratory biofeedback games. To validate these games, we compared breathing rate across 100 male participants (23 years ± 3.2 years) playing biofeedback and audio pacing versions of these games as well as a paced breathing app. The games were placed between repeat runs of a cognitively stressful Stroop-based task and the impact of the games on breathing and cognitive performance in the task also assessed. Our results showed that 1) differences in gameplay did not impact player performance; 2) biofeedback not only led to better breath control during play but also during the subsequent cognitively stressful task; and 3) biofeedback led to better attentional-cognitive performance in the subsequent task. Our multi-game experiments show that using respiratory biofeedback in video games is an effective strategy to learn paced breathing—on par with the standalone technique of paced breathing—and to self-regulate stress levels in later stressful scenarios. Furthermore, owing to its entertainment value, our relaxation solution has the potential to be more engaging and accessible than standalone paced breathing, for use over longer durations.
Fraud/Privacy Protection in Anonymous Auction (2007)

Most of current technologies that enable secure information sharing assume that entities that share information are mutually trustworthy. However, in recent applications this assumption is not realistic. As applications become sophisticated, information systems are required to share information securely even among untrustworthy entities. The problem is to keep the entities' credit card information confidential while ensuring fraud protection. This paper discusses one kind of problem about information sharing among untrustworthy entities, i.e. fraud protection in anonymous auctions.
Equal partners? Improving the integration between DSpace and Symplectic Elements (2015)

While self-submission by academics was regarded as the ideal way to add content to Open Repositories in the early days of such systems, the reality today is that many institutional repositories obtain their content automatically from integration with research management systems. The institutional DSpace repositories at Auckland University of Technology (AUT) and at the University of Waikato (UoW) were integrated with Symplectic Elements in 2010 (AUT) and in 2014 (UoW). Initial experiences at AUT suggested a mismatch between the interaction options offered to users of Symplectic Elements on one hand and the actions available to repository managers via the DSpace review workflow functionality on the other hand. Our presentation explores these mismatches and their negative effects on the repository as well as on the user experience. We then present the changes we made to the DSpace review workflow to improve the integration. We hope that our experiences will contribute to an improvement in the integration between repository software and research management systems.
Ultra wideband antenna of tilted triangular monopoles (2007)

In this paper, we propose two novel antennas for ceiling-mount base station applications. Conceptually, they are based on the self-complementary principle, but overcome the mentioned drawbacks of such antennas. Two slightly different topologies with triangular monopoles are presented to improve the impedance matching and the pattern stability across the operating bandwidth from 1 to 5.5 GHz. Therefore, both experimental and computational results of the antennas impedance and radiating properties are shown.
An Albino Mutant in Brassica rapa Maps to the PDX2 Locus on Chromosome 10 (2019)

We have identified an albino mutant in the plant Brassica rapa. This recessive mutation could provide insights into the photosynthetic pathways of all plants. Previously the mutation was mapped to chromosome 10 of Brassica rapa. To narrow down the chromosomal region containing the albino mutation, we grew a segregating population of plants. DNA was extracted from albino and wildtype (green) plants and genotyped using PCR markers on chromosome 10. The genotype detected using the INDEL2 marker perfectly predicted whether a plant was albino or WT. This indicates that the INDEL2 marker is tightly linked to the albino mutation. INDEL2 is near the gene PDX2 and we detected a single nucleotide change near the PDX2 gene that is only found in albino plants. It is possible that this mutation affects expression of PDX2 and is the cause of the albino phenotype. PDX2 is involved in vitamin B6 synthesis and it is unclear how altering vitamin metabolism could affect photosynthesis.
Maximal load demand allocation (1992)

The authors address the problem of determining the maximum amount of active and reactive unserved load demand that can be connected to each bus in an electric power system without violation of its operating constraints. This maximal load demand allocation problem, which is associated with each electrical island of a power system operating in a restorative state, is formulated as a mixed nonlinear-integer programming problem. A decoupling procedure partitions the overall allocation problem into a maximal active load demand allocation subproblem and a minimal reactive load demand deallocation subproblem. The approach has been implemented in the form of a computer program and tested using power system models of up to 118 buses. Details of the implementation procedure and some illustrative test results are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Induction of liquid crystalline phases in linear polyamines by complexation of transition metal ions (1998)

In this paper, we describe the preparation and characterization of polyamine–copper complexes based onN-alkylated polyethyleneimines which were obtained by polymer analogous reduction of the corresponding N-acylated polymers. Liquid crystalline properties of the originating linear polyamides are lost in the resulting polyamines which show a higher conformational mobility. In analogy to low molecular mass azacrown derivatives, the complexation of transition metal ions, here copper(ii), may reinduce liquid crystalline behavior. The structure formation in the liquid crystalline state is discussed based on X-ray investigations.
Baseline Demographics of aneurysms treated by stent-assisted coiling using the Enterprise or Neuroform stent. (2015)

&lt;p&gt;Numbers refer to aneurysms that were eventually coiled by stent assistance (n = 42 with Neuroform and n = 42 with Enterprise). Abbreviations: f (female), m (male), mm (millimeters), ant (anterior circulation), post (posterior circulation), SW (side wall), SD (standard deviation), OR (odds ratio), CI (confidence interval).&lt;/p&gt;
Software-defined data protection (2021)

Most modern data processing pipelines run on top of a distributed storage layer, and securing the whole system, and the storage layer in particular, against accidental or malicious misuse is crucial to ensuring compliance to rules and regulations. Enforcing data protection and privacy rules, however, stands at odds with the requirement to achieve higher and higher access bandwidths and processing rates in large data processing pipelines. In this work we describe our proposal for the path forward that reconciles the two goals. We call our approach "Software-Defined Data Protection" (SDP). Its premise is simple, yet powerful: decoupling often changing policies from request-level enforcement allows distributed smart storage nodes to implement the latter at line-rate. Existing and future data protection frameworks can be translated to the same hardware interface which allows storage nodes to offload enforcement efficiently both for company-specific rules and regulations, such as GDPR or CCPA. While SDP is a promising approach, there are several remaining challenges to making this vision reality. As we explain in the paper, overcoming these will require collaboration across several domains, including security, databases and specialized hardware design.
1. Alternative splicing of viral receptors: A review of the diverse morphologies and physiologies of adenoviral receptors. (2014)

Understanding the biology of cell surface proteins is important particularly when they are utilized as viral receptors for viral entry. By manipulating the expression of cell surface receptors that have been coopted by viruses, the susceptibility of an individual to virus-induced disease or, alternatively, the effectiveness of viral-based gene therapy can be modified. The most commonly studied vector for gene therapy is adenovirus. The majority of adenovirus types utilize the coxsackievirus and adenovirus receptor (CAR) as a primary receptor to enter cells. Species B adenovirus do not interact with CAR, but instead interact with the cell surface proteins desmoglein-2 (DSG-2) and cluster of differentiation 46 (CD46). These cell surface proteins exhibit varying degrees of alternative mRNA splicing, creating an estimated 20 distinct protein isoforms. It is likely that alternative splice forms have allowed these proteins to optimize their effectiveness in a plethora of niches, including roles as cell adhesion proteins and regulators of the innate immune system. Interestingly, there are soluble isoforms of these viral receptors, which lack the transmembrane domain. These soluble isoforms can potentially bind to the surface of a virus in the extracellular compartment, blocking the ability of the virus to bind to the host cell, reducing viral infectivity. Finally, the diversity of viral receptor isoforms appears to facilitate an assortment of interactions between viral receptor proteins and cytosolic proteins, leading to differential sorting in polarized cells. Using adenoviral receptors as a model system, the purpose of this review is to highlight the role that isoform-specific protein localization plays in the entry of pathogenic viruses from the apical surface of polarized epithelial cells.
Synthesis of ZnO Nanorods Arrays on ITO and Their Photoelectrochemical Performance (2009)

Synthesis of ZnO Nanorods Arrays on ITO and Their Photoelectrochemical Performance X. Q. Gu1 2, L. P. Zhu1 ∗, Z. Z. Ye1, X. L. Cui2, K. F. Huo2, and Paul K. Chu2 ∗ 1State Key Laboratory of Silicon Materials, Department of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China 2Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China