gebhart/patrepeval huggingface dataset:
Induction of mucosal immunity in cotton rats to haemagglutinin-esterase glycoprotein of bovine coronavirus by recombinant adenovirus. (1995)

An effective vaccine against enteric bovine coronavirus (BCV) must be able to induce mucosal immunity. We recently described the construction of recombinant human adenovirus type 5 (hAd5) carrying the BCV haemagglutinin-esterase (HE) gene in the early transcription region 3 of the adenovirus genome. In this study, we examined the induction of systemic and mucosal immune responses to the hAd5 vector carrying the BCV HE gene (AdBcHE) following intranasal or enteric immunization of cotton rats. Regardless of the route of administration, mucosal immunization with AdBcHE induced significant levels of anti-HE IgG antibodies in serum. In addition, following intranasal immunization with AdBcHE, significant levels of anti-HE IgA antibodies were found in lung washes of immunized cotton rats. Furthermore, the specific anti-HE antibodies in sera and mucosal secretions efficiently neutralized BCV infectivity in vitro. T-cell proliferation and cell-mediated cytotoxic responses against the BCV HE were elicited in the spleen of intranasally immunized animals. The results demonstrate that mucosal immunization with AdBcHE is capable of inducing both systemic and mucosal immunity to the BCV HE. These immune responses may be important in protecting animals from BCV infection.
A Recommendation System for Proactive Health Monitoring Using IoT and Wearable Technologies (2017)

Proactive monitoring of one's health could avoid serious diseases as well as better maintain the individual's well-being. In today's Internet of Things (IoT) world, there has been numerous wearable technological devices to monitor/measure different health attributes. With the increasing number of attributes and wearables, it becomes unclear to individuals which ones they should be using. The aim of this paper is to provide a novel recommendation engine for personalized advised wearables and IoT solutions for any given individual. The way the engine works is through first identifying the diseases that this person is at risk of, given his/her attributes and medical history. This is done via analyzing the individual's unstructured medical history using text mining, adding it to his/her structured demographic attributes, and then feeding this data to a machine learning classification model that predicts eventual diseases. Then, we map these diseases to the attributes that need to be measured in order to monitor them. Lastly, we use a mathematical optimization model that we developed to recommend the optimal wearable devices and IoT solutions for the individual. Thus, our solution enables proactive health monitoring and can thus provide a significant human benefit.
The viral polymerase inhibitor 7-deaza-2’- C -methyladenosine is a potent inhibitor of in vitro Zika virus replication and delays disease progression in a robust mouse infection model (2016)

Abstract Zika virus (ZIKV) is an emerging flavivirus typically causing a dengue-like febrile illness, but neurological complications, such as microcephaly in newborns, have potentially been linked to this viral infection. We established a panel of in vitro assays to allow the identification of ZIKV inhibitors and demonstrate that the viral polymerase inhibitor 7-deaza-2’- C -methyladenosine (7DMA) efficiently inhibits replication. Infection of AG129 (IFN-α/β and IFN-γ receptor knockout) mice with ZIKV resulted in acute neutrophilic encephalitis with viral antigens accumulating in neurons of the brain and spinal cord. Additionally, high levels of viral RNA were detected in the spleen, liver and kidney, and levels of IFN-γ and IL-18 were systematically increased in serum of ZIKV-infected mice. Interestingly, the virus was also detected in testicles of infected mice. In line with its in vitro anti-ZIKV activity, 7DMA reduced viremia and delayed virus-induced morbidity and mortality in infected mice, which also validates this small animal model to assess the in vivo efficacy of novel ZIKV inhibitors. Since AG129 mice can generate an antibody response, and have been used in dengue vaccine studies, the model can also be used to assess the efficacy of ZIKV vaccines. Article Summary Line: A robust cell-based antiviral assay was developed that allows to screen for and validate novel inhibitors of Zika virus (ZIKV) replication. The viral polymerase inhibitor 7-deaza-2’- C -methyladenosine (7DMA) was identified as a potent ZIKV inhibitor. A mouse model for ZIKV infections, which was validated for antiviral studies, demonstrated that 7DMA markedly delays virus-induced disease in this model.
Wavelength Conversion of 36QAM through Four-Wave Mixing in HNLF (2013)

We experimentally demonstrate wavelength conversion of a 50-Gbps 36QAM using four-wave mixing effect in highly-nonlinear fiber. Error free is experimentally achieved with a 0.3-dB power penalty at BER of 10−3 with respect to the input.
Response to: Cavagna et al The importance of considering cultural and environmental elements in an interventional model of care to fight hypertension in Africa (2021)

To the Editor, We appreciate the thoughtful interest from Dr Cavagna and colleagues in the Empower Health program. We applied human-centered design methodology when developing the model to ensure the application was locally and culturally appropriate.1, 2 Of course, the model does not discourage traditional medicine or other resources that could potentially further patient education and improve adherence behaviors. However, traditional medicine practice is often not standardized and does not adhere to nationally accepted guidelines for cardiovascular care. For example, about 21% of South African traditional herbal medicine patients used combinations of tea and other mixtures for the treatment of hypertension.3 Such herbal medicines might have unpredictable interactions with prescribed medications. Availability and accessibility of essential drugs remain a challenge in low- and lower-middle income countries and improving therapy access is an important role of the responsible health care system and governments.4 At least occasional problems obtaining prescribed medications were reported by 20% of hypertensive patients in a recent Ghanaian survey.5 Indeed, the supply of antihypertensive medications was temporarily interrupted during the pilot phase of the Empower Health program, although significant improvements in blood pressure were still achieved (Figure 1).2 While Kenya and Ghana are considered middle income countries, the population served by the model was mostly low-income and middle-income segments and in mostly remote rural settings. Both are representative of many Sub-Saharan countries with rural and urban populations that face similar challenges controlling hypertension. Note that smart phone ownership is not required in the model. Shared access via trained personnel or community health workers or location-based set-ups accommodate all patients including most patients who do not own a smartphone. Furthermore, the Empower Health model is currently available to over 20 000 patients in 2 countries, serving both public and private sectors and growing. We intend to continue to report program outcomes and have planned new randomized multi-center prospective studies. Based on this design and ongoing expansion, the Empower Health model is relevant to address low blood pressure control rates in many other African countries. FK, CL, and DH are full time employees of Medtronic Inc; RS has received consulting and speaker fees from Medtronic; all other authors report no competing interests. HAO, GY, CM, and DAH drafted the manuscript all authors reviewed, edited, and contributed materially to the final document.
Hemopred: A Web Server for Predicting the Hemolytic Activity of Peptides (2017)

A sequence-based predictor which is publicly available as the web service of HemoPred, is proposed to predict and analyze the hemolytic activity of peptides.
Cover Image, Volume 114, Number 10, October 2017 (2017)

Cover Legend: The cover image, by Yuta Kurashina et al., is based on the Article Enzyme-free cell detachment mediated by resonance vibration with temperature modulation, DOI 10.1002/bit.26361
Prediction of Left Ventricular Remodeling and Analysis of Infarct Resorption in Patients with Reperfused Myocardial Infarcts by Using Contrast-enhanced MR Imaging (2007)

Infarct size 24% or more of the LV area constitutes an important threshold to predict remodeling. Patients with remodeling develop disproportionate infarct resorption.
Evidence against Glycogen Cycling of Gluconeogenic Substrates in Various Liver Preparations (2002)

The effect of inhibition of glycogen phosphorylase by 1,4-dideoxy-1,4-imino-d-arabinitol on rates of gluconeogenesis, gluconeogenic deposition into glycogen, and glycogen recycling was investigated in primary cultured hepatocytes, in perfused rat liver, and in fed or fasted rats in vivo clamped at high physiological levels of plasma lactate. 1,4-Dideoxy-1,4-imino-d-arabinitol did not alter the synthesis of glycerol-derived glucose in hepatocytes or lactate-derived glucose in perfused liver or fed or fasted rats in vivo. Thus, 1,4-dideoxy-1,4-imino-d-arabinitol inhibited hepatic glucose output in the perfused rat liver (0.77 +/- 0.19 versus 0.33 +/- 0.09, p < 0.05), whereas the rate of lactate-derived gluconeogenesis was unaltered (0.22 +/- 0.09 versus 0.18 +/- 0.08, p = not significant) (1,4-dideoxy-1,4-imino-d-arabinitol versus vehicle, micromol/min * g). Overall, the data suggest that 1,4-dideoxy-1,4-imino-d-arabinitol inhibited glycogen breakdown with no direct or indirect effects on the rates of gluconeogenesis. Total end point glycogen content (micromol of glycosyl units/g of wet liver) were similar in fed (235 +/- 19 versus 217 +/- 22, p = not significant) or fasted rats (10 +/- 2 versus 7 +/- 2, p = not significant) with or without 1,4-dideoxy-1,4-imino-d-arabinitol, respectively. The data demonstrate no glycogen cycling under the investigated conditions and no effect of 1,4-dideoxy-1,4-imino-d-arabinitol on gluconeogenic deposition into glycogen. Taken together, these data also suggest that inhibition of glycogen phosphorylase may prove beneficial in the treatment of type 2 diabetes.
The Stratix™ 10 Highly Pipelined FPGA Architecture (2016)

This paper describes architectural enhancements in the Altera Stratix? 10 HyperFlex? FPGA architecture, fabricated in the Intel 14nm FinFET process. Stratix 10 includes ubiquitous flip-flops in the routing to enable a high degree of pipelining. In contrast to the earlier architectural exploration of pipelining in pass-transistor based architectures, the direct drive routing fabric in Stratix-style FPGAs enables an extremely low-cost pipeline register. The presence of ubiquitous flip-flops simplifies circuit retiming and improves performance. The availability of predictable retiming affects all stages of the cluster, place and route flow. Ubiquitous flip-flops require a low-cost clock network with sufficient flexibility to enable pipelining of dozens of clock domains. Different cost/performance tradeoffs in a pipelined fabric and use of a 14nm process, lead to other modifications to the routing fabric and the logic element. User modification of the design enables even higher performance, averaging 2.3X faster in a small set of designs.
N,N,N′,N′,N′′,N′′-Hexamethylguanidinium di-μ3-chlorido-tetra-μ2-chlorido-decachloridotetrabismuthate acetonitrile disolvate (2016)

The asymmetric unit of the solvated title compound, (C 7 H 18 N 3 ) 4 [Bi 4 Cl 16 ]·2CH 3 CN, comprises two cations, one half [Bi 4 Cl 16 ] 4− ion and one acetonitrile molecule. One N , N , N ′, N ′, N ′′, N ′′-hexamethylguanidinium ion shows orientational disorder and two sets of N- and C-atom positions were found, with an occupancy ratio of 0.941 (2):0.059 (2). The second cation is not disordered. The C—N bond lengths in the two guanidinium ions range from 1.334 (17) to 1.341 (17) Å, indicating double-bond character and pointing towards charge delocalization within the NCN planes. The four Bi III ions are coordinated by six chloride ions in distorted octahedral manner. Two [Bi 2 Cl 8 ] 2− dimers are fused together, forming a centrosymmetric tetranuclear [Bi 4 Cl 16 ] 4− cluster. The bond lengths of bismuth to the terminal chlorides [2.4982 (7)–2.5509 (6) Å] are shorter than those of the double and triply bridging ones [2.7052 (6)–3.0320 (6) Å]. The acetonitrile solvent molecule is disordered over two positions, with an occupancy ratio of 0.818 (4):0.182 (4) for the two orientations. The crystal structure is stabilized by a three-dimensional network of C—H...Cl hydrogen bonds.
Synthesis of Reverse Transcriptase Inhibitor Tenofovir (2015)

Key words tenofovir - reverse transcriptase inhibitors - regioselective acetal cleavage - phosphonomethyl ethers - bis(diethylamino)chlorophosphine
An experience report on extracting and viewing memory events via wireshark (2014)

Modern program analysis environments lack a principled method of monitoring low-level memory events. Such monitoring is of great value to activities like debugging, reverse engineering, vulnerability analysis, and security policy enforcement. Although current systems can be coerced to produce streams of memory events, most such techniques are inefficient or overly invasive and offer an unconstrained control over memory, which can subvert the reliability of such memory interposition as part of the attack engineering workflow.

Our system, Cage, is a kernel-level mechanism for monitoring the memory events of a process. Like several existing memory trapping systems, Cage modifies and uses the functionality of the Linux kernel memory page subsystem. Cage translates the memory activity of a process into a packet-like format, and these events are exported over a device. The memory event packets can be captured and displayed using an existing analyzer (Wireshark). At present, Cage can monitor the memory events for the data, stack, and heap of a process as well as arbitrarily cage any other memory region. We have caged a Gnome login session successfully and noticed no ill effects. We discuss several potential applications that arise from imposing this network packet metaphor on memory events.
An Enantioselective Formal Synthesis of Montelukast Sodium (2015)

A formal synthesis of the antiasthma drug montelukast sodium is described, wherein the key chiral diol intermediate was accessed with greater convergence of the C-C bond-forming steps as compared to previous routes. Improved synthetic efficiency was achieved by deploying homogeneous metal-based catalysis in two pivotal steps. In the first, a tandem Mizoroki-Heck reaction and double-bond isomerization between a previously known allyl alcohol intermediate and a hindered 2-(2-halophenyl)propan-2-ol secured direct access to the 3-(2-(2-hydroxypropan-2-yl)phenyl)-1-phenylpropan-1-one moiety in the product. In the second step, asymmetric hydrogenation of the ketone functionality in the Mizoroki-Heck reaction product provided a convenient method to introduce the benzylic alcohol chiral center and obtain the desired chiral diol precursor of montelukast sodium. A detailed catalyst screening led to the identification of ((R)-Xyl-BINAP)((R,R)-DPEN)RuCl2 as a catalyst that afforded an enantioselectivity of 99% ee in the hydrogenation step on a multigram lab scale at a molar substrate:catalyst loading of 5000:1.
Low-floor bus design preferences of walking aid users during simulated boarding and alighting (2012)

Low-floor buses represent a significant improvement in accessible public transit for passengers with limited mobility. However, there is still a need for research on the inclusive design of transit buses to identify specific low-floor bus design conditions that are either particularly accommodating or challenging for passengers with functional and mobility impairments. These include doorway locations, seating configuration and the large front wheel-well covers that collectively impact boarding, alighting and interior movement of passengers. Findings from a laboratory study using a static full-scale simulation of a lowfloor bus to evaluate the impact of seating configuration and crowding on interior movement and accessibility for individuals with and without walking aids are presented (n=41). Simulated bus journeys that included boarding, fare payment, seating, and alighting were performed. Results from video observations and subjective assessments showed differences in boarding and alighting performance and users' perceptions of task difficulty. The need for assistive design features (e.g. handholds, stanchions), legroom and stowage space for walking aids was evident. These results demonstrate that specific design conditions in low-floor buses can significantly impact design preference among those who use walking aids. Consideration of ergonomics and inclusive design can therefore be used to improve the design of low-floor buses.
Open Fractures of the Patella (1996)

We retrospectively reviewed 57 open patella fractures treated at our institution between 1976 and 1989. Forty-four patients with 47 fractures (cases) were available for follow-up a mean of 9.4 years after injury (range 2.2-15.7). High-energy vehicular trauma was the cause of injury in > 90% of cases. Treatment included osteosynthesis in 50% of cases and patellectomy (partial or total) in the remainder. At follow-up evaluation, results were excellent in 17% of cases, good in 60%, fair in 17%, and poor in 6%. Nonunion occurred in two cases in which nonrigid internal fixation was used. The incidence of deep infection was 10.7%, and the infection rate correlated with the magnitude of soft-tissue injury. Two of the seven fractures (29%) treated with cerclage wiring became infected. None of the open type I and II fractures treated with immediate internal fixation or primary wound closure (or both) became infected. Therefore, we recommend immediate rigid internal fixation (other than cerclage wiring) of types I and II open patella fractures. Partial patellectomy of highly comminuted fractures provided results similar to those of internal fixation of less comminuted fractures. Thus, when comminution precludes fixation, partial patellectomy can be performed without hesitation. The timing of wound closure should be individualized.
Reduction of DC-link capacitor in case of cascade multilevel converters by means of reactive power control (2014)

A new method to selectively control the amount of dc-link voltage ripple by processing the desired reactive power by a DC/DC converter in an isolated AC/DC or AC/DC/AC system is proposed. The concept can reduce the dc-link capacitors used for balancing the input and output power and thereby limiting the voltage ripple. It allows the use of a smaller dc-link capacitor and hence a longer lifetime and at the same time high power density and low cost can be achieved. The isolated DC/DC converter is controlled to process the desired reactive power in addition to the active power. The control system to achieve this selective degree of compensation is proposed and verified by Simulations.
Working Safely with H5N1 Viruses (2012)

Research on H5N1 influenza viruses has received much attention recently due to the possible dangers associated with newly developed avian H5N1 viruses that were derived from highly pathogenic avian viruses and are now transmissible among ferrets via respiratory droplets. An appropriate discussion, based on scientific facts about the risks that such viruses pose and on the biocontainment facilities and practices necessary for working safely with these viruses, is needed. Selecting the right level of biocontainment is critical for minimizing the risks associated with H5N1 research while simultaneously allowing an appropriately fast pace of discovery. Rational countermeasures for preventing the spread of influenza can be developed only by gaining a thorough knowledge of the molecular mechanisms at work in host specificity and transmission.
Optimization of immunoaffinity enrichment and detection: toward a comprehensive characterization of the phosphotyrosine proteome of K562 cells by liquid chromatography-mass spectrometry (2011)

Phosphorylation of protein tyrosine residues regulates many cell functions and has also been proved to be involved in oncogenesis. Thus, the identification of the phosphotyrosine (pTyr) proteome of cells is a very important task. Since tyrosine phosphorylation represents only around 1% of the total human phosphoproteome, the study of pTyr proteins is rather challenging. Here we report the optimization study of the phosphotyrosine proteome using K562 cells as a model system. A substantial segment of the phosphotyrosine proteome of K562 cells was characterized by immunoaffinity enrichment with 4G10 and PYKD1 antibodies followed by LC-MS/MS analysis. 480 non-redundant pTyr peptides corresponding to 342 pTyr proteins were found. 141 pTyr peptides were not described elsewhere. The mass spectrometry approach involving high-resolving FTMS analysis of precursor ions and subsequent detection of CID fragments in a linear ion trap was considered as optimal. For detection of low abundant pTyr peptides pooling of individual immunoaffinity enrichments for one LC-MS/MS analysis was crucial. The enrichment properties of the monoclonal PYKD1 antibody were presented for the first time, also in comparison to the 4G10 antibody. PYKD1 was found to be more effective for protein enrichment (1.2 and 5% efficiency at peptide and protein level correspondingly), while 4G10 showed better results when peptide enrichment was performed (15% efficiency versus 3.6% at protein level). Substantially different subsets of the phosphoproteome were enriched by these antibodies. This finding together with previous studies demonstrates that comprehensive pTyr proteome characterization by immunoprecipitation requires multiple antibodies to be used for the affinity enrichment.
ChemInform Abstract: A Michael Equilibration Model to Control Site Selectivity in the Condensation Toward Aminopyrazoles. (2015)

Abstract Conditions for the site‐selective condensation between hydrazines and alkoxy 2‐cyanoacrylates or their malononitrile counterparts are elaborated.
Embedding triple-modular redundancy into a hypercube architecture (1988)

This paper describes an embedding of Triple Modular Redundancy (TMR) into a binary hypercube. The goal is to improve fault tolerance by masking any single-point faults. Each module of an application task is triplicated and executed in parallel on three nodes of a 2-dimensional subcube (Q2) of the hypercube. Each of these nodes also executes a voter process. The remaining node is used for message passing only. All outputs from the triplicated modules are voted on, and the voting results are transmitted to the appropriate destination. Thus, all interunit messages are also triplicated.We propose an embedding of TMR into a hypercube which can be implemented in a manner transparent to the application program. Subcubes are allocated so that the address space for the TMR units is also a hypercube. Hence, the subcube allocation and intermodule communication schemes are defined to be analogous to the schemes used in the nonredundant system. The embedded system is proven to mask all single-point faults.
Novel venous thromboembolic disease (VTED) prophylaxis for total knee arthroplasty—aspirin and fish oil (2017)

This study demonstrated the potentially synergistic anti-thromboembolic effect of aspirin and fish oil in the prevention of post-operative venous thromboembolism in primary TKA patients. Based on the results from this study, the authors conclude that the combination of aspirin and fish oil maybe an excellent thromboprophylactic modality for patients to use after TKA. These results warrant further, larger prospective studies analyzing the use of fish oil supplements in VTE prophylaxis.