gebhart/patrepeval huggingface dataset:
Protein kinase CK2: a newcomer in the ‘druggable kinome’ (2006)

The acronym CK2 (derived from the misnomer 'casein kinase' 2) denotes one of the most pleiotropic members of the eukaryotic protein kinase superfamily, characterized by an acidic consensus sequence in which a carboxylic acid (or pre-phosphorylated) side chain at position n+3 relative to the target serine/threonine residue plays a crucial role. The latest repertoire of CK2 substrates includes approx. 300 proteins, but the analysis of available phosphopeptide databases from different sources suggests that CK2 alone may be responsible for the generation of a much larger proportion (10-20%) of the eukaryotic phosphoproteome. Although for the time being CK2 is not included among protein kinases whose inhibitors are in clinical practice or in advanced clinical trials, evidence is accumulating that elevated CK2 constitutive activity co-operates to induce a number of pathological conditions, including cancer, infectious diseases, neurodegeneration and cardiovascular pathologies. The development and usage of cell-permeant, selective inhibitors discloses a scenario whereby CK2 plays a global anti-apoptotic role, which under special circumstances may lead to untimely and pathogenic cell survival.
Human blindsight is mediated by an intact geniculo-extrastriate pathway (2015)

Although damage to the primary visual cortex (V1) causes hemianopia, many patients retain some residual vision; known as blindsight. We show that blindsight may be facilitated by an intact white-matter pathway between the lateral geniculate nucleus and motion area hMT+. Visual psychophysics, diffusion-weighted magnetic resonance imaging and fibre tractography were applied in 17 patients with V1 damage acquired during adulthood and 9 age-matched controls. Individuals with V1 damage were subdivided into blindsight positive (preserved residual vision) and negative (no residual vision) according to psychophysical performance. All blindsight positive individuals showed intact geniculo-hMT+ pathways, while this pathway was significantly impaired or not measurable in blindsight negative individuals. Two white matter pathways previously implicated in blindsight: (i) superior colliculus to hMT+ and (ii) between hMT+ in each hemisphere were not consistently present in blindsight positive cases. Understanding the visual pathways crucial for residual vision may direct future rehabilitation strategies for hemianopia patients.
Solution Structure and <i>In Silico</i> Binding of a Cyclic Peptide with Hepatitis <scp>B</scp> Surface Antigen (2013)

A specific ligand targeting the immunodominant region of hepatitis B virus is desired in neutralizing the infectivity of the virus. In a previous study, a disulfide constrained cyclic peptide cyclo S(1) ,S(9) Cys-Glu-Thr-Gly-Ala-Lys-Pro-His-Cys (S(1) , S(9) -cyclo-CETGAKPHC) was isolated from a phage displayed cyclic peptide library using an affinity selection method against hepatitis B surface antigen. The cyclic peptide binds tightly to hepatitis B surface antigen with a relative dissociation constant (KD (rel) ) of 2.9 nm. The binding site of the peptide was located at the immunodominant region on hepatitis B surface antigen. Consequently, this study was aimed to elucidate the structure of the cyclic peptide and its interaction with hepatitis B surface antigen in silico. The solution structure of this cyclic peptide was solved using (1) H, (13) C, and (15) N NMR spectroscopy and molecular dynamics simulations with NMR-derived distance and torsion angle restraints. The cyclic peptide adopted two distinct conformations due to the isomerization of the Pro residue with one structured region in the ETGA sequence. Docking studies of the peptide ensemble with a model structure of hepatitis B surface antigen revealed that the cyclic peptide can potentially be developed as a therapeutic drug that inhibits the virus-host interactions.
Human periodontal ligament: a niche of neural crest stem cells (2008)

This research provides evidence that human periodontal ligament, in addition to its mesodermal derivatives, produces neural crest-like cells. Such features suggest a recapitulation of their embryonic state. The human periodontal ligament revealed itself as a viable alternative source for possible primitive precursors to be used in stem-cell therapies.
The village/commune safety policy and HIV prevention efforts among key affected populations in Cambodia: finding a balance (2012)

The Village/Commune Safety Policy was launched by the Ministry of Interior of the Kingdom of Cambodia in 2010 and, due to a priority focus on "cleaning the streets", has created difficulties for HIV prevention programs attempting to implement programs that work with key affected populations including female sex workers and people who inject drugs. The implementation of the policy has forced HIV program implementers, the UN and various government counterparts to explore and develop collaborative ways of delivering HIV prevention services within this difficult environment. The following case study explores some of these efforts and highlights the promising development of a Police Community Partnership Initiative that it is hoped will find a meaningful balance between the Village/Commune Safety Policy and HIV prevention efforts with key affected populations in Cambodia.
Physics of the microwave oven (2003)

This is the first of two articles about the physics of microwave ovens. This article deals with the generation of microwaves in the oven and includes the operation of the magnetrons, waveguides and standing waves in resonant cavities. It then considers the absorption of microwaves by foods, discussing the dielectric relaxation of water, penetration depths of electromagnetic waves in matter and, in considering the possible chemical changes during the microwave heating, multi-photon ionization or dissociation.
Attelia: Reducing user's cognitive load due to interruptive notifications on smart phones (2015)

In today's ubiquitous computing environment where the number of devices, applications and web services are ever increasing, human attention is the new bottleneck in computing. To minimize user cognitive load, we propose Attelia, a novel middleware that identifies breakpoints in user interaction and delivers notifications at these moments. Attelia works in realtime and uses only the mobile devices that users naturally use and wear, without any modifications to applications, and without any dedicated psycho-physiological sensors. Our evaluation proved the effectiveness of Attelia. A controlled user study showed that notifications at detected breakpoint timing resulted in 46% lower cognitive load compared to randomly-timed notifications. Furthermore, our “in-the-wild” user study with 30 participants for 16 days further validated Attelia's value, with a 33% decrease in cognitive load compared to randomly-timed notifications.
Silencing the Morphogenesis of Rotavirus (2004)

The morphogenesis of rotaviruses follows a unique pathway in which immature double-layered particles (DLPs) assembled in the cytoplasm bud across the membrane of the endoplasmic reticulum (ER), acquiring during this process a transient lipid membrane which is modified with the ER resident viral glycoproteins NSP4 and VP7; these enveloped particles also contain VP4. As the particles move towards the interior of the ER cisternae, the transient lipid membrane and the nonstructural protein NSP4 are lost, while the virus surface proteins VP4 and VP7 rearrange to form the outermost virus protein layer, yielding mature infectious triple-layered particles (TLPs). In this work, we have characterized the role of NSP4 and VP7 in rotavirus morphogenesis by silencing the expression of both glycoproteins through RNA interference. Silencing the expression of either NSP4 or VP7 reduced the yield of viral progeny by 75 to 80%, although the underlying mechanism of this reduction was different in each case. Blocking the synthesis of NSP4 affected the intracellular accumulation and the cellular distribution of several viral proteins, and little or no virus particles (neither DLPs nor TLPs) were assembled. VP7 silencing, in contrast, did not affect the expression or distribution of other viral proteins, but in its absence, enveloped particles accumulated within the lumen of the ER, and no mature infectious virus was produced. Altogether, these results indicate that during a viral infection, NSP4 serves as a receptor for DLPs on the ER membrane and drives the budding of these particles into the ER lumen, while VP7 is required for removing the lipid envelope during the final step of virus morphogenesis.
Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant (2020)

Abstract Background The role of aerosols in the transmission of SARS-CoV-2 remains debated. We analysed an outbreak involving three non-associated families in Restaurant X in Guangzhou, China, and assessed the possibility of aerosol transmission of SARS-CoV-2 and characterize the associated environmental conditions. Methods We collected epidemiological data, obtained a video record and a patron seating-arrangement from the restaurant, and measured the dispersion of a warm tracer gas as a surrogate for exhaled droplets from the suspected index patient. Computer simulations were performed to simulate the spread of fine exhaled droplets. We compared the in-room location of subsequently infected cases and spread of the simulated virus-laden aerosol tracer. The ventilation rate was measured using the tracer decay method. Results Three families (A, B, C), 10 members of which were subsequently found to have been infected with SARS-CoV-2 at this time, or previously, ate lunch at Restaurant X on Chinese New Year’s Eve (January 24, 2020) at three neighboring tables. Subsequently, three members of family B and two members of family C became infected with SARS-CoV-2, whereas none of the waiters or 68 patrons at the remaining 15 tables became infected. During this occasion, the ventilation rate was 0.75–1.04 L/s per person. No close contact or fomite contact was observed, aside from back-to-back sitting by some patrons. Our results show that the infection distribution is consistent with a spread pattern representative of exhaled virus-laden aerosols. Conclusions Aerosol transmission of SARS-CoV-2 due to poor ventilation may explain the community spread of COVID-19.
Shizukaol D, a Dimeric Sesquiterpene Isolated from Chloranthus serratus, Represses the Growth of Human Liver Cancer Cells by Modulating Wnt Signalling Pathway (2016)

Natural products have become sources of developing new drugs for the treatment of cancer. To seek candidate compounds that inhibit the growth of liver cancer, components of Chloranthus serratus were tested. Here, we report that shizukaol D, a dimeric sesquiterpene from Chloranthus serratus, exerted a growth inhibition effect on liver cancer cells in a dose- and time-dependent manner. We demonstrated that shizukaol D induced cells to undergo apoptosis. More importantly, shizukaol D attenuated Wnt signalling and reduced the expression of endogenous Wnt target genes, which resulted in decreased expression of β-catenin. Collectively, this study demonstrated that shizukaol D inhibited the growth of liver cancer cells by modulating Wnt pathway.
Balanced metric labeling (2005)

We define the balanced metric labeling problem, a generalization of the metric labeling problem, in which each label has a capacity, i.e., at most l vertices can be assigned to it. The balanced metric labeling problem is a generalization of fundamental problems in the area of approximation algorithms, e.g., arrangements and balanced partitions of graphs. It is also motivated by resource limitations in certain practical scenarios. We focus on the case where the given metric is uniform and note that this case alone encompasses various well-known graph partitioning problems. We present the first (pseudo) approximation algorithm for this problem, achieving for any ε, 0 < ε < 1, an approximation factor of O((ln n)/ε), while assigning at most min {O(ln k)/1 - ε, l + 1| ( 1 + ε) l vertices to each label (k is the number of labels). Our approximation algorithm is based on a novel randomized rounding of a linear programming formulation that combines an embedding of the graph in a simplex together with spreading metrics and additional constraints that strengthen the formulation. Our randomized rounding technique uses both a randomized metric decomposition technique and a randomized label assignment technique. At the heart of our approach is the fact that only limited dependency is created between the labels assigned to different vertices, allowing us to bound the expected cost of the solution and the number of vertices assigned to each label, simultaneously. We note that the number of vertices assigned to each label is bounded via a new inequality of Janson[15] for tail bounds of (partly) dependent random variables.
Latex allergy in primary care providers. (2011)

The prevalence of latex allergy in this study was 5.9%. The importance of a firm diagnosis at the onset of symptoms should be stressed, since reducing contact with latex can yield negative test results. Assessment of IgE reactivity to the individual latex allergens (component-resolved diagnosis) can detect sensitization to panallergens such as profilin and help to clarify the diagnosis.
Constructing STR Multiplex Assays (2004)

Multiplex polymerase chain reaction (PCR) refers to the simultaneous amplification of multiple regions of deoxyribonucleic acid (DNA) using PCR. Commercial short tandem repeat (STR) assays that can coamplify as many as 16 different loci have become widely used in forensic DNA typing. This chapter will focus on some of the aspects of constructing robust STR multiplex assays, including careful design and quality control of PCR primers. Examples from the development of a cat STR 12plex and a human Y chromosome STR 20plex are used to illustrate the importance of various parts of the protocol. Primer design parameters and Internet-accessible resources are discussed, as are solutions to problems with residual dye artifacts that result from impure primers.
Up‐regulation of β‐chemokines and down‐modulation of CCR5 co‐receptors inhibit simian immunodeficiency virus transmission in non‐human primates (2000)

A non-cognate mechanism of protection against human immunodeficiency virus-1 (HIV-1) infection involves up-regulation of beta-chemokines, which bind and may down-modulate the CCR5 co-receptors, thereby preventing transmission of M-tropic HIV-1. The objective of this investigation was to evaluate this mechanism in vivo in non-human primates. Rhesus macaques were immunized by a modified targeted lymph nodes (TLN) route with recombinant simian immunodeficiency virus (SIV) glycoprotein 120 (gp120) and p27 in alum, and adsorbed recombinant granulocyte-macrophage colony-stimulating factor (GM-CSF) with either interleukin (IL)-2 or IL-4. Immunization induced significant increases in the concentrations of CD8 cell-derived suppressor factor (CD8-SF), regulated on activation normal T cells expressed and secreted (RANTES), macrophage inflammatory protein (MIP)-1alpha and MIP-1beta, and down-modulation of the proportion of cells expressing CCR5 (r = 0.737, P<0.05). The macaques were then challenged with SIVmac 220 by the rectal mucosal route. The plasma SIVmac RNA showed a significant inverse correlation with the CD8-SF or the concentration of the three beta-chemokines (r = 0.831 and 0.824, P<0.01), but a positive correlation between the proportion of CCR5+ cells and SIVmac RNA (r = 0.613, P = 0.05). These results demonstrate for the first time in vivo that immunization up-regulates beta-chemokines, which may down-modulate CCR5 co-receptors, and both functions are significantly correlated with the viral load. Hence, the non-cognate beta-chemokine-CCR5 mechanism should be considered as complementary to specific immunity in vaccination against HIV.
The B.Sc. (N) graduate as a nurse practitioner. (1974)

Since the beginning of the basic baccalaureate programme in McGill University, the overall goal has been to prepare nurses who are capable of giving thoughtful nursing care to patients in any situation.
 The curriculum was devised to ensure sufficient science content not only to fulfill the requirements for the degree, but also to enable the student to develop a scientific approach to nursing. The emphasis is on the way the student learns to nurse rather than on the nursing skills she acquires. This, to us, is the key to baccalaureate education in nursing. It also allows us to say that our graduates have potential as nurse practitioners that will help them to develop nursing in response to the need for health services.
Resource utilization and total cost of care among Medicare advantage patients with metastatic pancreatic cancer receiving NCCN category 1 preferred regimens. (2022)

531 Background: Medicare Advantage accounts for almost 40% of Medicare beneficiaries in 2021. There is limited research evaluating utilization and cost for Medicare Advantage patients with metastatic pancreatic cancer (m-PANC) receiving various NCCN Category 1 preferred regimens. Methods: We used ICD-10 diagnosis codes to identify patients with m-PANC without end-stage renal disease in the 2016-2019 Milliman Consolidated Health Cost Guidelines Sources Database (CHSD) claims files. Study patients had 2+ claims with a pancreatic cancer diagnosis and Medicare Advantage coverage for 3 months pre- and 1 month post-metastasis diagnosis. Patients with stand-alone Part D plan coverage or aged<65 years were excluded. Total cost of care (TCOC) was the sum of the average paid by the insurer and patient. Study patients were treated with NCCN Category 1 preferred regimens: 1L gemcitabine/nab-paclitaxel (gem/nab), 1L gemcitabine monotherapy (gem mono), 1L FOLFIRINOX (FFX), and 2L+ liposomal irinotecan (5FU was not included in this analysis; see Limitations for further details). Results: Of the approximately 2.5 million patients covered by Medicare Advantage in CHSD, there were 946 patients that received an NCCN Category 1 chemotherapy regimen between 2016 and 2019. Among NCCN Category 1 preferred regimens, patients receiving 2L+ liposomal irinotecan had the lowest mean admissions per beneficiary and mean readmission rate (0.5 and 8%) compared to patients receiving gem/nab (0.8 and 12%), gem mono (0.6 and 8%), or FFX (0.6 and 9%). Patients receiving 2L+ liposomal irinotecan also had the shortest length of stay per inpatient admission in days (2.9) compared to patients receiving gem/nab (5.1), gem mono (3.6), or FFX (4.3). Mean claims per beneficiary for emergency department observations was lowest among patients receiving 2L+ liposomal irinotecan (0.7), compared to patients receiving gem/nab (0.9), gem mono (1.0), or FFX (0.89). Patients receiving 2L+ liposomal irinotecan had lower median TCOC ($31,885) than patients receiving gem/nab ($39,479) or FFX ($32,632). Conclusions: Patients with Medicare Advantage receiving 2L+ liposomal irinotecan-based regimens to treat m-PANC had lower healthcare resource utilization in key categories and lower median total costs than patients receiving other NCCN Category 1 preferred regimens. Limitations: Analysis of different populations or time periods may yield different results. Our study used claims data and not electronic health records (EHRs), so we could not control for clinical covariates. Patient characteristics and regimen performance might influence which regimens patients receive. We did not adjust TCOC or utilization for LOT durations. We did not study whether liposomal irinotecan-based therapy patients received concomitant 5FU or prior gemcitabine-based therapy.
Correction for Zhang et al., “Nanopore-Targeted Sequencing Improves the Diagnosis and Treatment of Patients with Serious Infections” (2023)

Volume 14, no. 1, e03055-22, 2023, https://doi.org/10.1128/mbio.03055-22. Page 11, last two lines: “this study was approved by the Ethics Committee of Wuhan Union Hospital.” should read “this study was approved by the Ethics Committee of Wuhan Union Hospital under ethics approval number [2023] No.0170.”
TMC-89A and B, New Proteasome Inhibitors from Streptomyces sp. TC 1087. (2000)

The ubiquitin/proteasome system is a major pathway of selective protein degradation in eukaryotic cells. The pp.967
Effect of annealing on the structure and magnetic properties of graphite encapsulated nickel and cobalt nanocrystals (1998)

We report the structure and magnetic studies of carbon coated nanocrystals of nickel and cobalt synthesized in a special low carbon to metal ratio arc chamber. Powder x-ray diffraction profiles show peaks associated with single phase of fcc nickel or cobalt and major peaks of graphite with no evidence of carbides or solid solutions of carbon in the metal. Measured lattice spacing of crystalline particles and that of graphite coating from high-resolution transmission electron microscope images also confirm such findings. Magnetization measurements as a function of temperature in the range 20–900 °C give a Curie temperature equal to that of bulk metal within the experimental error. Upon heating and recooling of the particles a larger magnetization as high as 57% of bulk Co and 53% of bulk Ni was measured. Also M–H hysteresis loop of the particles have been measured at room temperature after annealing in the temperature range 20–650 °C for Ni, and 20–900 °C for Co. The dependence of room temperature saturation magnetization, remanent magnetization, and coercive field of the particles on annealing temperature is reported. These data are described by transition of particles form single domain to multidomain as a result of particle growth due to annealing. We also present the particle size distribution measurements that show log-normal behavior, and indicate substantial particle size growth due to annealing.
Software architecture of broadband distribution in the optical CATV network (2002)

This paper presents the OAM (operations, administration and maintenance) software architecture of the BRDS (broadband distribution subsystem) for an optical CATV network. We built an optical CATV network called SWAN (socio-cultural welfare advanced network) based on SDH (synchronous digital hierarchy) and FTTH (fiber to the home) technology. The BRDS is one of the SWAN subsystems. The OAM software of the BRDS consists of operating systems and application software. We describe the technical issues such as the implementation aspects, the development environment and the future plan of the OAM software for the BRDS.
Automated explosive detection systems based upon CT technology (2002)

CT has established itself as superior technology over conventional X-rays initially in medical imaging and now for explosive detection system (EDS) applications. What is true for anatomical structures of the human body is also true for baggage: cross-sectional images improve greatly the detection probability of specific structures. The challenges of transitioning CT from medical to EDS applications include the development of a new market as well as technical, environmental and operational issues. This paper explains automatic detection, which has not been done for medical applications yet. The approach taken went through feasibility study, supporting the definition of EDS standards, prototype development, and extensive airport trials. Threat detection required new algorithms to be invented which make use of the density and other topological information provided by CT. Today, operator intervention has been reduced to a small percentage of the luggage to make a decision on a threat. More automation is desirable in principle, and the current technical limits to detection and false alarm rates are discussed.