gebhart/patrepeval huggingface dataset:
The Structure of the Membrane Protein of SARS-CoV-2 Resembles the Sugar Transporter semiSWEET (2020)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the disease COVID-19 that has decimated the health and economy of our planet. The virus causes the disease not only in people but also in companion and wild animals. People with diabetes are at risk of the disease. As yet we do not know why the virus is highly successful in causing the pandemic within 3 months of its first report. The structural proteins of SARS include, membrane glycoprotein (M), envelope protein (E), nucleocapsid protein (N) and the spike protein (S). The structure and function of the most abundant structural protein of SARS-CoV-2, the membrane (M) glycoprotein is not fully understood. Using in silico analyses we determined the structure and potential function of the M protein. The M protein of SARS-CoV-2 is 98.6% similar to the M protein of bat SARS-CoV, maintains 98.2% homology with pangolin SARS-CoV, and has 90% homology with M protein of SARS-CoV; whereas, the similarity was only 38% with the M protein of MERS-CoV. In silico analyses showed that the M protein of SARS-CoV-2 has a triple helix bundle, form a single 3-transmembrane domain (TM), and are homologous to the prokaryotic sugar transport protein semiSWEET. SemiSWEETs are related to the PQ-loop family that function as cargo receptors in vesicle transport, mediates movement of basic amino acids across lysosomal membranes, and is also involved in phospholipase flippase function. The advantage and role of the M protein having a sugar transport-like structure is not clearly understood. The M protein of SARS-CoV-2 interacts with S, E and N protein. The S protein of the virus is glycosylated. It could be hypothesized that the sugar transporter-like structure of the M protein influences glycosylation of the S protein. Endocytosis is critical for the internalization and maturation of RNA viruses, including SARS-CoV-2. Sucrose is involved in endosome and lysosome maturation and may also induce autophagy, pathways that help in the entry of the virus. Overall, it could be hypothesized that the semiSWEET sugar transporter-like structure of the M protein may be involved in multiple functions that may aid in the rapid proliferation, replication and immune evasion of the SARS-CoV-2 virus. Biological experiments would validate the presence and function of the semiSWEET sugar transporter.
Synthetic Chemistry with N-Acyliminium Ions derived from Piperazine-2,5-diones and Related Compounds (2013)

The ubiquity of the piperazine-2,5-dione core (2,5-diketopiperazine, DKP) in natural products and the preponderance of this heterocyclic framework in many bioactive compounds have encouraged the development of methods for the selective functionalization of readily available piperazine-2,5-dione substrates. C-functionalization using DKPs as electrophilic glycine templates is generally mediated by N-acyliminium ions. These intermediates show highly versatile reactivities, which are reflected in an impressive number of synthetic applications. However, even in some highly comprehensive treatments of Nacyliminium ions, references to the construction of these species on piperazine-2,5-dione frameworks are scarce. The present review aims at filling this gap, placing emphasis upon the construction of endocyclic and exocyclic acyliminium ions derived from piperazine-2,5- diones and their synthetic applications. More complex structures that include this framework as a structural fragment, such as pyrazino[1,2-b]isoquinoline-1,4-diones or pyrazino[2,1- b]quinazoline-3,6-diones, are also overviewed.
[Perioperative radiographic reconstruction of the scoliotic vertebral column]. (1999)

We have developed a new per-operative three dimensional (3D) reconstruction technique to evaluate the 3D correction of a scoliotic spine induced by surgery using Cotrel-Dubousset instrumentation. A small object with 15 embedded markers was used to calibrate the radiographic system. During surgery, the calibration object was sterilized and fixed to the patient just before the acquisition of two pairs of posterior-anterior and sagittal radiographs; one pair before the rotation maneuver of the rod and one pair after the maneuver. The markers were digitized on each radiograph and their relative 3D positions were measured to establish the relation between the 3D positions of the anatomical structures and their 2D positions on the radiographs. This relation was used to calculate the 3D position of six anatomical landmarks per vertebra (the centers of the superior and inferior vertebral body endplates and the proximal and distal bodies of both pedicles) from the identification of these landmarks on each radiograph. We made a 3D representation of the thoracic and lumbar spine of three patients with idiopathic scoliosis undergoing corrective surgery by the posterior approach. Clinical indices (Cobb angle, axial rotation and the plane of maximum curvature) computed from the 3D reconstruction of the spine obtained before and after the rotation maneuver of the rod were compared to evaluate the 3D correction performed during the surgery. The new proposed approach allows the surgeon to evaluate the per-operative shape of the spine. This approach is simpler, faster and less risky for the patient than the previous method which employed an electromagnetic digitizer to measure the 3D coordinates of anatomical landmarks located on the posterior part of the spine. Furthermore, the 3D representation of the spine visualized from different points of view gives the surgeon an accurate evaluation of the 3D correction during the surgical procedure.
A Comparison Study of Magnetic Bearing Controllers for a Fully Suspended Dynamic Spin Rig (2002)

NASA Glenn Research Center (GRC) has developed a fully suspended magnetic bearing system for the Dynamic Spin Rig (DSR) that is used to perform vibration tests of turbomachinery blades and components under spinning conditions in a vacuum. Two heteropolar radial magnetic bearings and a thrust bearing and the associated control system were integrated into the DSR to provide noncontact magnetic suspension and mechanical excitation of the 35 lb vertical rotor with blades to induce turbomachinery blade vibration. A simple proportional-integral-derivative (PID) controller with a special feature for multidirectional radial excitation worked very well to both support and shake the shaft with blades. However, more advanced controllers were developed and successfully tested to determine the optimal controller in terms of sensor and processing noise reduction, smaller rotor orbits, and energy savings for the system. The test results of a variety of controllers we demonstrated up to the rig's maximum allowable speed of 10,000 rpm are shown.
A NEW MATHEMATICAL MODEL FOR THE WORKOVER RIG SCHEDULING PROBLEM (2016)

One of the most important activities in the oil and gas industry is the intervention in wellsfor maintenance services, which is necessary to ensure the constant production of oil. These interventions are carried out by workover rigs. Thus, the Workover Rig Scheduling Problem (WRSP) consists of finding the best schedule to service the wells while considering the limited number of rigs with the objective of minimizing the total production loss. In this study, a 0-1 integer linear programming model capable of efficiently solving the WRSP with a homogeneous fleet of rigs is proposed. Computational experiments were carried out using instances based on real cases in Brazil to compare the results obtained by the proposed model with the results reported by other methods. The proposed model was capable of solving all instances considered in a reduced computational time, including the large instances for which only approximatesolutions were presently known.
Internet multicast routing and transport control protocols (2002)

Multicasting is a mechanism to send data to multiple receivers in an efficient way. We give a comprehensive survey on network and transport layer issues of Internet multicast. We begin with an introduction to the current Internet protocol multicast model-the "host group" model and the current Internet multicast architecture, then discuss in depth the following three research areas: (1) scalable multicast routing; (2) reliable multicast; and (3) multicast flow and congestion control. Our goal is to summarize the state of the art in Internet multicast and to stimulate further research in this area.
Abstract 1036: ARC synergizes with ABT-737 to induce apoptosis in human cancer cells (2010)

Abstract Previously, we reported that the nucleoside analog/transcriptional inhibitor ARC was able to induce p53-independent apoptosis in multiple cancer cell lines of different origin. This occurred at least in part by the suppression of Mcl-1 expression, which a short-lived, pro-survival member of the Bcl-2 family. Interestingly, pan-caspase inibitor Z-VAD-FMK protected leukemia cells from ARC-induced mitochondrial damage and apoptosis, and Mcl-1 mRNA and protein from down-regulation by ARC. At the same time treatment of human cancer cells with the pan-Bcl-2 inhibitor ABT-737 alone led to up-regulation of Mcl-1 protein expression. Combination of sub-apoptotic concentrations of ABT-737 and ARC suppressed Mcl-1 expression, induced mitochondrial injury and potent apoptosis in wide variety of human cancer cell lines. In prostate cancer cells co-treatment with ARC and ABT-737 resulted in synergistic induction of cell death with combination index 0.7-0.8. These data suggest that ABT-737/ARC combination that simultaneously targets Bcl-2 and Mcl-1 may be efficient against human cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1036.
A CMOS infrared optical preamplifier with a variable-gain transimpedance amplifier (2005)

A CMOS infrared wireless optical receiver front-end is described. A feedback analysis is carried out for the design of a stable variable-gain transimpedance feedback amplifier. A current-mode amplifier, exhibiting a low input resistance and a high output resistance, is designed. The current amplifier is employed as the feedforward gain element of a variable-gain fully-differential transimpedance feedback amplifier. For an infrared wireless optical receiver front-end employing the transimpedance amplifier, the optical preamplifier achieves a transimpedance gain of 87dB/spl Omega/, a bandwidth of 135MHz with a 5pF photodiode capacitance, and a power consumption of 28mW.
A Group Activity Trial for Adults with Pervasive Developmental Disorder in a Psychiatric Day Hospital (2015)

青年期以降にはじめて広汎性発達障害の診断を受ける者が増加しているが，支援を受ける必要性がわからず社会資源の利用に繋がらない例も多い。筆者らはこのような患者を対象に精神科デイケアにおいて，疾患・就労・社会参加に向けた情報提供と患者個別の特徴への気づきを促す目的で，全22回のグループ活動を試みた。活動の開始時と終了時に個人面談を行い，患者個別の特徴を共有した。また，各活動は目標提示した上で開始し，「まとめシート」を用いて振り返り，実践的な活動を積極的に導入し，患者が個別の特徴に気づく工夫を行った。活動開始時，何らかの社会資源を利用している者は少なかったが，終了後には様々な社会資源を利用し，就労に向けた具体的な行動がみられた。精神科デイケアがもつリハビリ機能が患者の活動性を高め，患者自身が「相談や支援を受ける」体験をしたこともその後の社会資源の利用に繋がったと考えられた。
Incidence and Predictors of Early and Late Mortality After Transcatheter Aortic Valve Implantation in 663 Patients With Severe Aortic Stenosis (2011)

Benefit of TAVI with the CoreValve Revalving System is maintained over time up to 1 year, with acceptable mortality rates at various time points. Although procedural complications are strongly associated with early mortality at 30 days, comorbidities and postprocedural paravalvular aortic regurgitation ≥ 2+ mainly impact late outcomes between 30 days and 1 year.
Attitudinal barriers hindering adoption of Telepsychiatry among mental healthcare professionals: Israel as a case-study (Preprint) (2021)

<sec> <title>BACKGROUND</title> Despite obvious and proven advantages for the use of telemedicine in psychiatry, mental healthcare professionals have shown deep-seated mistrust and suspicion of telepsychiatry, which hinders its widespread application. </sec> <sec> <title>OBJECTIVE</title> The current study aims to examine the attitudes of Israeli mental health professionals towards telepsychiatry; seeking to uncover the relationship with experience with telepsychiatry, and organizational affiliation. </sec> <sec> <title>METHODS</title> A qualitative study, including 27 in-depth interviews with Israeli mental-health professionals, representing a diverse analytical, geographical, and gendered cross-section of the local professional community. A thematic analysis revealed three major themes – economic efficiency, clinical quality, and the effects on the work-life balance of healthcare professionals. Individuals’ responses were furthermore compared against hierarchical position, organizational affiliation, and experience with telepsychiatry. </sec> <sec> <title>RESULTS</title> Participants were evenly divided, between supporters of telepsychiatry and those who oppose and object to its widespread usage in routine mental healthcare. This division manifested itself most clearly in their assessment of the clinical quality of telepsychiatry. However, it was also palpable in their assessment of its efficiency and its effects for healthcare professionals. Furthermore, the study also revealed a positive correlation between participants’ experience with telepsychiatry, and their support for its usage. However, this relationship seems to be mitigated by one’s employment and organizational affiliations. Employees of at least one Israeli Health Maintenance Organization exhibited a negative trendline, where more experience with telepsychiatry also meant stronger opposition for its utilization. </sec> <sec> <title>CONCLUSIONS</title> Attitudes of mental health professionals were found to be widely divergent and sharply dichotomized regarding different aspects of telepsychiatry, and its suitability for mental healthcare services. However, there was general consensus that telemedicine may not fulfil its promise of being a panacea to the problems of modern public medicine. At the same time, attitudes were related to hierarchical position, organizational affiliation and personal experience with telepsychiatry. Specifically, organizational affiliation influenced experience with and support for assimilation of telepsychiatry. The study also revealed the role of organizational leadership and culture in promoting or inhibiting the proliferation and adoption of innovative technologies and services in modern medicine. </sec>
Linear Complexitv and Random Sesuences (1986)

The problem of characterizing the randomness of finite sequences arises in cryptographic applications. The idea of randomness clearly reflects the difficulty of predicting the next digit of a sequence from all the previous ones. The approach taken in this paper is to measure the {linear) unpredictability of a sequence (finite or periodic) by the length of the shortest linear feedback shift register (LFSR) that is able to generate the given sequence. This length is often referred to in the literature as the linear comDlexitv of the sequence. It is shown that the expected linear complexity of a sequence of n independent and uniformly distributed binary random variables is very close to n/2 and, that the variance of the linear complexity is virtually independent of the sequence length, i.e. is virtually a constant! For the practically interesting case of periodically repeating a finite truly random sequence of length Zm or 2m-1, it is shown that the linear complexity is close to the period length.
Just a graze? Cephalic tetanus presenting as a stroke mimic (2013)

A 76-year-old right handed woman awoke with sudden onset of difficulty with swallowing, slurred speech and left-sided facial weakness and numbness. She had multiple vascular risk factors: hypertension, hypercholesterolaemia, impaired glucose tolerance and a 50 pack-year smoking history. Twelve days before presentation she had developed right-sided facial weakness. Ten days before presentation she had sustained a right supraorbital laceration which required suturing after falling on to pavement (figure 1). A CT scan of the head at the time of injury was normal (figure 2). On examination, there was left-sided upper motor neurone facial palsy and right lower motor neurone facial palsy, with dysarthria but no dysphasia, diminished sensation over the left maxillary and mandibular areas, and normal limb examination. Given her constellation of signs, we considered the possibility of brainstem stroke and recent right Bell's palsy.



Figure 1 
Star-shaped right supraorbital laceration sustained 10 days before presentation during a road traffic accident. This is the wound from which Clostridium tetani was eventually cultured. This photograph was taken after the wound was further debrided and post decannulation, as evidenced by her tracheostomy scar.





Figure 2 
Axial CT scan of head post injury shows a large extracranial soft tissue swelling overlying the frontal bones, particularly on the right side and extending inferiorly into the right periorbital region. Tiny radiopaque densities within this extracranial soft tissue swelling raise the possibility of foreign bodies. The ventricular system and basal cisterns are normal.



CT scan of head and CT angiogram showed a large right supraorbital haematoma, but no acute stroke (figure 3 …
Synthesis of a Potent Cathepsin S Inhibitor Labeled with Deuterium and Carbon-14 (2012)

Morpholine-4-carboxylic acid {(S)-1-[4-cyano-1-(3-morpholin-4-yl-propyl)-piperidin-4-ylcarbamoyl]-4,4- dimethyl-hexyl}-amide, (1) is a potent reversible and selective cathepsin S inhibitor. Deuterium labeled (1) was prepared in four steps in 62% overall yield from [2H8]- morpholine and chiral acid (6). Carbon-14 labeled (1) was obtained in two steps using sodium [14C]-cyanide in a modified Strecker reaction followed by amide bond formation with acid (6) in 74% overall radiochemical yield. The phosphate salt of this compound was produced by treatment with phosphoric acid in methanol in 97% yield.
Micronized Purified Flavonoid Fraction and the Treatment of Chronic Venous Insufficiency: Microcirculatory Mechanisms (2000)

The standard treatments for venous diseases of the lower limb include compression bandaging and stockings as well as surgical removal of varicose veins. There is a number of conditions in which these conventional treatments are ineffective, particularly in the management of leg ulceration. Drug treatments for healing venous leg ulcers have yet to be developed to the stage of good clinical efficacy, but may assist in the management of patients. Flavonoid drugs have been widely used in the management of the symptoms of venous disease for many years and have recently been studied in some detail to assess their effects on the microcirculation. Work in animal models of ischemia/reperfusion (I/R) show that micronized purified flavonoid fraction (MPFF) modulates leukocyte adhesion and prevents endothelial damage. Similar biochemical effects have been observed in patients with venous disease and may explain the efficacy of this drug in the management of edema and other symptoms of venous disease. There is some evidence that MPFF promotes venous leg ulcer healing.
Ethnopharmacological Survey and Comparative Study of the Healing Activity of Moroccan Thyme Honey and Its Mixture with Selected Essential Oils on Two Types of Wounds on Albino Rabbits (2021)

Wound healing consists of several continuous phases involving various cells and chemical intermediates. As a rich source of nutrition elements, honey has proved to have potential benefits in the treatment of various diseases. The present study was designed to investigate the healing effect of a honey mixture with selected essential oils on chemical and thermal wound models in rabbits. Dressing mixtures of <i>Thymus vulgaris</i> honey with three essential oils (<i>Origanum vulgare, Rosmarinus officinalis,</i> and <i>Thymus vulgaris</i>) were prepared and applied daily in the treatment groups. These essential oils were rich in phytochemicals and had significant antibacterial activity against four selected ATCC bacterial strains. Madecasol ointment was used as a standard control. The healing effect of the mixtures was evaluated by measuring wound surface area and comparing healing time. The results showed that the healing rate in the treatment groups was significantly higher than that of the untreated group and standard group. The best healing effect for burns was seen in the mixture of honey and <i>Thymus vulgaris</i> essential oil, which had wound closure rates of 85.21% and 82.14% in thermal- and chemical-induced burns, respectively, and showed the shortest healing time (14 days) in comparison to other groups. Therefore, it can be concluded that honey mixtures have significant beneficial effects on skin wound healing and, thus, they may be used as a healing agent in different types of wounds in humans after specific clinical trials.
Impact of optical flexibility and sub-band switching on multi-layer transport network architectures (2014)

We present how it is possible to still increase the global capacity of the currently deployed 100 Gbps based multi-layer transport networks thanks to the introduction of the sub-wavelength switching concept on future flexible optical add-drop multiplexers (FOADM). Such concept relies on the capabilities of the flexible node to adjust the optical channel characteristics to the service demand requirements. The technical solution uses coherent orthogonal frequency-division multiplexing as modulation to manage, with a very fine granularity, sub-wavelength optical switching. Multi-band techniques create super-channel to gather sub-wavelength together in order to increase the optical channel transmission capacity up to ultra-high data rate such as 1 Tbps. After having demonstrated performances of the solution, we evaluate, through typical use cases, the opportunity to introduce such flexible networking concept in future multi-layer transport networks and detail its advantages in terms of aggregation. Beyond techno-economic comparisons, the study integrates operational constraints and outlines the basis of future optical network planning.
Draft Genome Sequence of a Novel Thermofilum sp. Strain from a New Zealand Hot Spring Enrichment Culture (2018)

A draft genome of a new <i>Thermofilum</i> sp. strain was obtained from an enrichment culture metagenome. Like its relatives, <i>Thermofilum</i> sp. strain NZ13 is adapted to organic-rich thermal environments and has to depend on other organisms and the environment for some key amino acids, purines, and cofactors.
Chemical modification of electrodes (1983)

In this paper the methods of preparing and characterizing chemically modified electrodes are outlined, and several applications are described. From State-of-the-Art Symposium: Electrochemistry, ACS meeting, Kansas City, 1982.
Presence of alveolar macrophages as a criterion for determining the suitability of sputum specimens for bacterial culture. (1984)

The microscopic and bacteriological findings in paired saliva and sputum specimens from 66 patients with chronic bronchitis were compared in order to determine whether the presence of alveolar macrophages is a valid criterion for determining the suitability of a sputum specimen for bacterial culture. Alveolar macrophages were mainly present in sputum specimens, the culture results of which differed from the culture results of the matching saliva specimen (p less than 0.001). Sputum specimens containing alveolar macrophages appeared to be contaminated less with oropharyngeal flora than specimens which did not contain alveolar macrophages. Potential pathogens such as Streptococcus pneumoniae and Haemophilus influenzae were isolated only from sputum specimens containing alveolar macrophages. It is concluded that the presence of alveolar macrophages indicates that sputum originates from the lower respiratory tract. The results also showed that the presence of leukocytes in sputum may be considered significant if alveolar macrophages are also present.