gebhart/patrepeval huggingface dataset:
Herpesvirus systematics (2010)

This paper is about the taxonomy and genomics of herpesviruses. Each theme is presented as a digest of current information flanked by commentaries on past activities and future directions. The International Committee on Taxonomy of Viruses recently instituted a major update of herpesvirus classification. The former family Herpesviridae was elevated to a new order, the Herpesvirales, which now accommodates 3 families, 3 subfamilies, 17 genera and 90 species. Future developments will include revisiting the herpesvirus species definition and the criteria used for taxonomic assignment, particularly in regard to the possibilities of classifying the large number of herpesviruses detected only as DNA sequences by polymerase chain reaction. Nucleotide sequence accessions in primary databases, such as GenBank, consist of the sequences plus annotations of the genetic features. The quality of these accessions is important because they provide a knowledge base that is used widely by the research community. However, updating the accessions to take account of improved knowledge is essentially reserved to the original depositors, and this activity is rarely undertaken. Thus, the primary databases are likely to become antiquated. In contrast, secondary databases are open to curation by experts other than the original depositors, thus increasing the likelihood that they will remain up to date. One of the most promising secondary databases is RefSeq, which aims to furnish the best available annotations for complete genome sequences. Progress in regard to improving the RefSeq herpesvirus accessions is discussed, and insights into particular aspects of herpesvirus genomics arising from this work are reported.
Regulated phosphorylation and low abundance of HeLa cell initiation factor eIF-4F suggest a role in translational control. Heat shock effects on eIF-4F. (1987)

Initiation factor eIF-4F, a multiprotein cap binding protein complex, was purified from HeLa cells by m7G affinity chromatography and independently by phosphocellulose column chromatography. The m7G affinity-purified sample contains three major proteins, p220, eIF-4A, and p28 (also known as CBP-I or eIF-4E). The abundancies of these proteins are roughly 2, 10, and 0.8 X 10(6) molecules/cell, respectively. Two-dimensional isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the eIF-4F samples shows that p28 comprises two isoelectric variants, one of which labels with phosphate and disappears when samples are treated with alkaline phosphatase. The 45,000-dalton protein in eIF-4F appears to be identical to eIF-4A. The p220 subunit rarely produces discrete spots on two-dimensional gel electrophoresis; in purified samples it usually forms 3 closely spaced streaks. eIF-4F fractionated by phosphocellulose chromatography separates into forms containing either phosphorylated or unphosphorylated p28. However, both fractions possess similar specific activities in in vitro translation assays for eIF-4F activity. The phosphorylation of p28 decreases upon heat shock when protein synthesis is repressed. The correlation of dephosphorylation of p28 with the inhibition of protein synthesis and the relatively low abundance of the eIF-4F complex suggest that eIF-4F plays a role in the translational control of mRNA binding. Limitations of the in vitro assay system may account for the failure to detect phosphorylation-dependent activity differences.
High mobility group box 1 (HMGB1) protein: possible amplification signal in the pathogenesis of falciparum malaria (2004)

High mobility group box 1 (HMGB1) protein, a DNA-binding protein that can also act as a pro-inflammatory cytokine if released from cells, is an important amplification signal in various forms of inflammation. The concentration of HMGB1 in serum taken at admission was increased in falciparum malaria in sixteen African children, more so in fatal cases than in those who subsequently recovered (P<0.001). Serum from both non-fatal (P=0.0048) and fatal (P<0.001) cases contained significantly more circulating HMGB1 than did serum from healthy Caucasian adults. These data provide an additional argument that malaria is fundamentally a systemic inflammatory state. In keeping with its developing role in sepsis, HMGB1 may enhance and prolong the inflammatory processes, and thus illness, in malaria.
Transforming Growth Factor‐β Inhibition and Endothelin Receptor Blockade in Rats with Monocrotaline‐Induced Pulmonary Hypertension (2012)

Transforming growth factor-β (TGF-β) inhibition is an investigational therapy for pulmonary arterial hypertension with promising results in experimental studies. The present work compared this approach with endothelin-receptor blockade and evaluated the effects of combined administration. Pulmonary arterial hypertension was induced by single monocrotaline injection (60 mg/kg) in 75 Wistar rats and 15 rats served as controls. Intervention groups consisted of treatment with an antibody against TGF-β-ligand, bosentan, both or none, initiated four weeks after monocrotaline injection. Right ventricular systolic pressure, pulmonary vascular remodeling, and exercise tolerance were evaluated eight weeks after monocrotaline injection. Either treatment, alone or in combination, lowered mortality. Comparable efficacy was found in the three treatment groups in terms of right ventricular systolic pressure (~45% decrease) and hypertrophy (~30% decrease), as well as exercise capacity. The three treatment groups equally ameliorated pulmonary vascular remodeling, evidenced by decreased vessel-wall thickness (in vessels 50-200 μm) and a smaller number of pre-capillary arterioles (< 50 μm) with a muscularized media. Treatment either with an antibody against TGF-β or with endothelin receptor blockade are equally effective in experimental pulmonary hypertension. Their combination provides no added benefit, indicating common mechanisms of action.
PbS quantum-dot doped glasses as saturable absorbers for mode locking of a Cr:forsterite laser (1997)

Quantum confined nanocrystals of PbS in glass were used as intracavity saturable absorbers to obtain passive continuous-wave mode locking in a Cr:forsterite laser. We obtained near transformed-limited 4.6 ps laser pulses at 110 MHz repetition rate, and a wide tunability range of 1207–1307 nm. The absorption saturation intensity of the quantum-dot PbS doped glasses was measured to be 0.2 MW/cm2.
Rapid label-free DNA analysis in picoliter microfluidic droplets using FRET probes (2009)

We report a novel microfluidic system that is capable of rapidly detecting DNA and its mutants in microfluidic droplets, in addition to elucidating the dynamic hybridization process. This microfluidic picoliter droplet analysis system is able to overcome the limitations of conventional analytical techniques that utilize immobilized sensing probes on a substrate. Molecular beacon (MB), a fluorescence resonance energy transfer (FRET) molecule, was used as the DNA sensing probe in picoliter droplets. The MB-DNA duplex formation process was analyzed by the change in FRET signal, which was acquired by the time-resolved method: converting distance traveled to hybridization time. This technique demonstrates the ability to detect presence of target nucleic acids within few seconds, multiplex DNA samples in microdroplet, and distinguish single nucleotide polymorphisms. It is promising for analyzing biomolecules or reactions, such as mRNA, cells, enzymatic activity, and protein folding whose analysis requires rapid mixing and small volume.
Missing in Action: The speed hump at Clement & 36th (2013)

Gambling disorder is an addiction that can cause major suffering, and some populations seem to be more vulnerable than others. Offender populations have a remarkably high prevalence of gambling problems and they are also over-represented in a number of diagnoses related to gambling disorder, like substance use disorders and antisocial personality disorder. Yet, there are few studies investigating gambling disorder prevalence and related psychiatric comorbidity in this group. This study aims to investigate the prevalence of, and association between, gambling disorder and other psychiatric diagnoses in a sample of young, male violent offenders. Two hundred and sixty-four male offenders, all serving sentences for violent crimes (recruited between 2010 and 2012) participated in this study and went through comprehensive psychiatric evaluation, including assessment for Diagnostic and Statistical Manual of Mental Disorders 4th Edition criteria. Sixteen percent of the participants met criteria for gambling disorder. Antisocial personality disorder, cannabis, cocaine and anabolic steroids abuse were significantly more common among participants with gambling disorder. The gambling disorder group also showed significantly lower educational attainment. Cocaine abuse and failure to graduate elementary and middle school in expected time were independently associated with gambling disorder in a regression analysis. This study confirms the previously described high prevalence of gambling disorder in offenders. The psychiatric comorbidity was high and the problems had started early, with lower educational attainment in the gambling disorder group. The findings stress the importance of increased awareness of gambling problems among convicted offenders and of gambling research on young people with delinquent behavior. There is a need of more research to investigate this further, in order to develop preventive strategies and treatment.
The genetic variation of the human HMGB1 gene (2007)

High-mobility group box 1 protein (HMGB1) is a nuclear DNA-binding protein, which also functions as a pleiotropic cytokine, implicated in the pathology of several different immune-mediated diseases. The purpose of this study was to examine the HMGB1 gene for putative polymorphisms in 103 healthy Caucasian Danish blood donors. A total of six polymorphisms and four mutations were identified in the HMGB1 gene. Subsequent MatInspector estimation revealed that several polymorphisms might have a potential regulatory impact on HMGB1 transcription. This study has characterized genetic variations in the HMGB1 gene locus, which may have a regulating role in the expression of HMGB1, providing the basis for molecular investigations of the HMGB1 gene in different disease settings.
Interleukin-9 stimulates the proliferation of human myeloid leukemic cells (1996)

Human interleukin-9 (IL-9) stimulates the proliferation of primitive hematopoietic erythroid and pluripotent progenitor cells, as well as the growth of selected colony-stimulating factor (CSF)-dependent myeloid cell lines. To further address the role of IL-9 in the development of acute leukemia, we evaluated the proliferative response of three leukemic cell lines and 32 primary samples from acute myeloblastic leukemia (AML) patients to recombinant human (rh)-IL-9 alone and combined with rh-IL-3, granulocyte-macrophage CSF (GM-CSF), and stem cell factor ([SCF] c-kit ligand). The colony-forming ability of HL60, K562, and KG1 cells and fresh AML cell populations upon IL-9 stimulation was assessed by a clonogenic assay in methylcellulose, whereas the cell-cycle characteristics of leukemic samples were determined by the acridine-orange flow cytometric technique and the bromodeoxyuridine (BRDU) incorporation assay. In addition, the terminal deoxynucleotidyl transferase assay (TDTA) and standard analysis of DNA cleavage by gel electrophoresis were used to evaluate induction of prevention of apoptosis by IL-9. Il-9, as a single cytokine, at various concentrations stimulated the colony formation of the three myeloid cell lines under serum-containing and serum-free conditions, and this effect was completely abrogated by anti-IL-9 monoclonal antibodies (MoAbs). When tested on fresh AML samples, optimal concentrations of IL-9 resulted in an increase of blast colony formation in all the cases studied (mean +/- SEM: 19 +/- 10 colony-forming unit-leukemic [CFU-L]/10(5) cells plated in control cultures v 107 +/- 32 in IL-9-supplemented dishes, P < .02). IL-9 stimulated 36.8% of CFU-L induced by phytohemagglutinin-lymphocyte-conditioned medium (PHA-LCM), and it was the most effective CSF for promoting leukemic cell growth among those tested in this study (i.e., SCF, IL-3, and GM-CSF). The proliferative activity of IL-9 was also observed when T-cell-depleted AML specimens were incubated with increasing concentrations of the cytokine. Addition of SCF to IL-9 had an additive or synergistic effect of the two cytokines in five of eight AML cases tested for CFU-L growth (187 +/- 79 colonies v 107 +/- 32 CFU-L, P = .05). Positive interaction was also observed when IL-9 was combined with IL-3 and GM-CSF. Studies of cell-cycle distribution of AML samples demonstrated that IL-9 alone significantly augmented the number of leukemic cells in S-phase in the majority of cases evaluated. IL-9 and SCF in combination resulted in a remarkable decrease of the G0 cell fraction (38.2% +/- 24% v 58.6% +/- 22% of control cultures, P < .05) and induced an increase of G1- and S-phase cells. Conversely, neither IL-9 alone nor the combination of IL-9 and SCF had any effect on induction or prevention of apoptosis of leukemic cells. In summary, our results indicate that IL-9 may play a role in the development of AML by stimulating leukemic cells to enter the S-phase rather than preventing cell death. Moreover, IL-9 acts synergistically with SCF for recruiting quiescent leukemic cells in cell cycle.
Correction: Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity (2013)

Small drug molecules usually bind to multiple protein targets or even unintended off-targets. Such drug promiscuity has often led to unwanted or unexplained drug reactions, resulting in side effects or drug repositioning opportunities. So it is always an important issue in pharmacology to identify potential drug-target interactions (DTI). However, DTI discovery by experiment remains a challenging task, due to high expense of time and resources. Many computational methods are therefore developed to predict DTI with high throughput biological and clinical data. Here, we initiatively demonstrate that the on-target and off-target effects could be characterized by drug-induced in vitro genomic expression changes, e.g. the data in Connectivity Map (CMap). Thus, unknown ligands of a certain target can be found from the compounds showing high gene-expression similarity to the known ligands. Then to clarify the detailed practice of CMap based DTI prediction, we objectively evaluate how well each target is characterized by CMap. The results suggest that (1) some targets are better characterized than others, so the prediction models specific to these well characterized targets would be more accurate and reliable; (2) in some cases, a family of ligands for the same target tend to interact with common off-targets, which may help increase the efficiency of DTI discovery and explain the mechanisms of complicated drug actions. In the present study, CMap expression similarity is proposed as a novel indicator of drug-target interactions. The detailed strategies of improving data quality by decreasing the batch effect and building prediction models are also effectively established. We believe the success in CMap can be further translated into other public and commercial data of genomic expression, thus increasing research productivity towards valid drug repositioning and minimal side effects.
Internalization of Mycobacterium bovis, Bacillus Calmette Guerin, by bladder cancer cells is cytotoxic (2007)

Instillation of Bacillus Calmette Guerin (BCG) into the bladder is the standard treatment for superficial bladder cancer. It leads to a local inflammatory response due to the release of cytokines and influx of immune cells to the tumor site. Although the presence of an intact immune system is an essential criterion for successful therapy, attachment of the bacteria to the bladder urothelial is just as important. The purpose of our study is to determine the role of bacterial internalization by epithelial cells. Transfection of the alpha5 integrin gene into the BCG unresponsive bladder cancer cell line, RT4, caused an increase in bacterial uptake and also increased cell death. Treatment of cells with cycloheximide did not prevent bacterial internalization but blocked its cytotoxic effect suggesting that unlike cell death, the process of bacterial internalization does not require new protein synthesis. Our data also show that the bacteria secretory products can prevent its own internalization. The extract prepared from lyophilized BCG altered the phosphorylation status of the focal adhesion kinase which is responsible for cellular endocytosis. Therefore, bacterial phosphatases may be present in the bacterial extract. Their activity may inhibit BCG internalization. Thus washing the reconstituted bacteria to remove the enzymes before instillation into the bladder might improve the therapeutic outcome of intravesical BCG therapy.
A Parametric Frequency Increased Power Generator for Scavenging Low Frequency Ambient Vibrations (2009)

This paper presents the design, fabrication, and testing of a miniature electromagnetic inertial power generator for scavenging low-frequency non-periodic vibrations. A bi-stable mechanical structure is used to initiate high-frequency mechanical oscillations in an electromagnetic scavenger. Because of the fixed internal displacement of this architecture, power density is improved and miniaturization can be achieved, while accommodating large amplitude vibrations. The fabricated device generated a peak power of 288μW and an average power of 5.8μW from an input acceleration of 9.8m/s2 at 10Hz. The device operates over a frequency range of 20Hz. The internal volume of the generator is 2.1cm3 (3.7cm3 including casing), half of a standard AA battery.
Long-term Durability of Sacral Nerve Stimulation Therapy for Chronic Fecal Incontinence (2013)

The therapeutic effect and improved quality of life for fecal incontinence is maintained 5 years after sacral nerve stimulation implantation and beyond. Device revision, replacement, or explant rate was acceptable, but future efforts should be aimed at improvement.
Synthesis of Diverse Indene Derivatives from 1-Diazonaphthalen-2(1H)-ones via Thermal Cascade Reactions (2013)

A sequential Wolff rearrangement of 1-diazonaphthalen-2(1H)-ones followed by trapping of the ketene intermediate with primary and aromatic amines or alcohols and phenols in the presence of various aldehydes generates 1H-indene-3-carboxamides or 1H-indene-3-carboxylates. This constitutes an unprecedented three-component coupling reaction that allows for the synthesis of functionalized indene derivatives under catalyst-free thermal conditions.
Small molecule obatoclax (GX15-070) antagonizes MCL-1 and overcomes MCL-1-mediated resistance to apoptosis (2007)

Elevated expression of members of the BCL-2 pro-survival family of proteins can confer resistance to apoptosis in cancer cells. Small molecule obatoclax (GX15-070), which is predicted to occupy a hydrophobic pocket within the BH3 binding groove of BCL-2, antagonizes these members and induces apoptosis, dependent on BAX and BAK. Reconstitution in yeast confirmed that obatoclax acts on the pathway and overcomes BCL-2-, BCL-XL-, BCL-w-, and MCL-1-mediated resistance to BAX or BAK. The compound potently interfered with the direct interaction between MCL-1 and BAK in intact mitochondrial outer membrane and inhibited the association between MCL-1 and BAK in intact cells. MCL-1 has been shown to confer resistance to the BCL-2/BCL-XL/BCL-w-selective antagonist ABT-737 and to the proteasome inhibitor bortezomib. In both cases, this resistance was overcome by obatoclax. These findings support a rational clinical development opportunity for the compound in cancer indications or treatments where MCL-1 contributes to resistance to cell killing.
The IL-6/sIL-6R complex as a novel target for therapeutic approaches (2007)

IL-6 plays a pivotal role in immune responses and certain oncologic conditions. The intense investigation of its biological activity and function led to the discovery of two different IL-6-driven signalling pathways. Binding to the membrane-bound IL-6 receptor (mIL-6R, CD126) causes the recruitment of two gp130 co-receptor molecules (CD130) and the activation of intracellular signalling cascades via gp130. Although this classical pathway is mainly limited to hepatocytes, neutrophils, monocytes/macrophages and certain other leukocyte populations, which express IL-6R on their surface, an alternative mechanism has also been described. Proteolytic cleavage of the mIL-6R protein or translation from alternatively spliced mRNA leads to the generation of a soluble form of the IL-6R (sIL-6R), which is likewise able to bind to IL-6. The resulting IL-6/sIL-6R complex is also capable of binding to gp130 and inducing intracellular signalling. Through this so-called 'trans-signalling' mechanism, IL-6 is able to stimulate cells that lack an endogenous mIL-6R. High levels of IL-6 and sIL-6R have been reported in several chronic inflammatory and autoimmune diseases as well as in cancer. Preclinical animal disease models have provided strong evidence that specific blockade of IL-6-regulated signalling pathways represents a promising approach for the therapy of these diseases. An optimised variant of the recently described fusion protein sgp30Fc is now heading towards its clinical evaluation.
The Beck operation in the treatment of angina pectoris. (1967)

<h3>Context</h3> Central to appropriate palliative care management in hospital settings is ensuring an adequately trained workforce. In order to achieve optimum palliative care delivery, it is first necessary to create a baseline understanding of the level of palliative care education and support needs among all clinical staff (not just palliative care specialists) within the acute hospital setting. <h3>Objectives</h3> The objectives of the study were to explore clinical staff: perceptions concerning the quality of palliative care delivery and support service accessibility, previous experience and education in palliative care delivery, perceptions of their own need for formal palliative care education, confidence in palliative care delivery and the impact of formal palliative care training on perceived confidence. <h3>Methods</h3> A purposive sample of clinical staff members (598) in a 710-bed hospital were surveyed regarding their experiences of palliative care delivery and their education needs. <h3>Results</h3> On average, the clinical staff rated the quality of care provided to people who die in the hospital as ‘good’ (x̄=4.17, SD=0.91). Respondents also reported that 19.3% of their time was spent caring for end-of-life patients. However, only 19% of the 598 respondents reported having received formal palliative care training. In contrast, 73.7% answered that they would like formal training. Perceived confidence in palliative care delivery was significantly greater for those clinical staff with formal palliative care training. <h3>Conclusions</h3> Formal training in palliative care increases clinical staff perceptions of confidence, which evidence suggests impacts on the quality of palliative care provided to patients. The results of the study should be used to shape the design and delivery of palliative care education programmes within the acute hospital setting to successfully meet the needs of all clinical staff.