gebhart/patrepeval huggingface dataset:
Inhibition of prostate carcinoma establishment and metastatic growth in mice by an antiangiogenin monoclonal antibody (2002)

A neutralizing monoclonal antibody (MAb) 26-2F to human angiogenin, a potent inducer of neovascularization, has been shown previously to prevent or delay the appearance of angiogenin-secreting human colon, fibrosarcoma and lung tumor cell xenografts implanted subcutaneously (s.c.) into athymic mice. In an analogous model system, we report here that the antibody also prevents the establishment of PC-3 androgen-independent human prostate cancer tumors in, on average, 40% of treated mice (p < 0.0001, survivor analysis). Intriguingly, combining MAb 26-2F together with cisplatin and suramin, 2 therapeutic agents that together showed little antitumor activity in the aforementioned model, resulted in an even greater degree of protection (71% protected, p = 0.009 compared to antibody treatment alone). This protective effect persisted several weeks after cessation of treatment. Additionally, prophylactic systemic administration of MAb 26-2F dramatically reduced by 50% the formation of spontaneous regional metastasis originating from primary growth in the prostate gland of PC-3M cells, highly metastatic variants of PC-3. Protection from metastasis was still significant when treatment with MAb 26-2F was delayed until after the primary tumor was well established. The antibody is not directly cytotoxic to either cell type, both of which secrete angiogenin in vitro and when growing as tumors in vivo, but changes the pattern of vascularity in primary tumors growing orthotopically. These findings, together with the observation that angiogenin protein and mRNA are apparently overexpressed in cancerous vs. normal human prostate tissues, demonstrate that angiogenin antagonism represents a promising new approach for preventing progression and metastasis of clinical prostate cancer.
Face masks effectively limit the probability of SARS-CoV-2 transmission (2021)

Airborne transmission by droplets and aerosols is important for the spread of viruses. Face masks are a well-established preventive measure, but their effectiveness for mitigating SARS-CoV-2 transmission is still under debate. We show that variations in mask efficacy can be explained by different regimes of virus abundance and related to population-average infection probability and reproduction number. For SARS-CoV-2, the viral load of infectious individuals can vary by orders of magnitude. We find that most environments and contacts are under conditions of low virus abundance (virus-limited) where surgical masks are effective at preventing virus spread. More advanced masks and other protective equipment are required in potentially virus-rich indoor environments including medical centers and hospitals. Masks are particularly effective in combination with other preventive measures like ventilation and distancing.
Influenza A: understanding the viral life cycle. (2009)

Influenza A virus belongs to the family of Orthomyxoviridae. It is an enveloped virus with a negative sense RNA segmented genome that encodes for 11 viral genes. This virus has evolved a number of mechanisms that enable it to invade host cells and subvert the host cell machinery for its own purpose, that is, for the sole production of more virus. Two of the mechanisms that the virus uses are "cap-snatching" and preventing the host cell from expressing its own genes. This mini-review provides a brief overview as to how the virus is able to invade host cells, replicate itself, and exit the host cell.
Prediction of EF‐hand calcium‐binding proteins and analysis of bacterial EF‐hand proteins (2006)

The EF-hand protein with a helix-loop-helix Ca(2+) binding motif constitutes one of the largest protein families and is involved in numerous biological processes. To facilitate the understanding of the role of Ca(2+) in biological systems using genomic information, we report, herein, our improvement on the pattern search method for the identification of EF-hand and EF-like Ca(2+)-binding proteins. The canonical EF-hand patterns are modified to cater to different flanking structural elements. In addition, on the basis of the conserved sequence of both the N- and C-terminal EF-hands within S100 and S100-like proteins, a new signature profile has been established to allow for the identification of pseudo EF-hand and S100 proteins from genomic information. The new patterns have a positive predictive value of 99% and a sensitivity of 96% for pseudo EF-hands. Furthermore, using the developed patterns, we have identified zero pseudo EF-hand motif and 467 canonical EF-hand Ca(2+) binding motifs with diverse cellular functions in the bacteria genome. The prediction results imply that pseudo EF-hand motifs are phylogenetically younger than canonical EF-hand motifs. Our prediction of Ca(2+) binding motifs provides not only an insight into the role of Ca(2+) and Ca(2+)-binding proteins in bacterial systems, but also a way to explore and define the role of Ca(2+) in other biological systems (calciomics).
Paired Restricted Boltzmann Machine for Linked Data (2016)

Restricted Boltzmann Machines (RBMs) are widely adopted unsupervised representation learning methods and have powered many data mining tasks such as collaborative filtering and document representation. Recently, linked data that contains both attribute and link information has become ubiquitous in various domains. For example, social media data is inherently linked via social relations and web data is networked via hyperlinks. It is evident from recent work that link information can enhance a number of real-world applications such as clustering and recommendations. Therefore, link information has the potential to advance RBMs for better representation learning. However, the majority of existing RBMs have been designed for independent and identically distributed data and are unequipped for linked data. In this paper, we aim to design a new type of Restricted Boltzmann Machines that takes advantage of linked data. In particular, we propose a paired Restricted Boltzmann Machine (pRBM), which is able to leverage the attribute and link information of linked data for representation learning. Experimental results on real-world datasets demonstrate the effectiveness of the proposed framework pRBM.
Modulation of Kaposi's Sarcoma-Associated Herpesvirus Infection and Replication by MEK/ERK, JNK, and p38 Multiple Mitogen-Activated Protein Kinase Pathways during Primary Infection (2006)

Kaposi's sarcoma-associated herpesvirus (KSHV) is etiologically associated with Kaposi's sarcoma, a dominant AIDS-related tumor of endothelial cells, and several other lymphoproliferative malignancies. While activation of the phosphatidylinositol 3-kinase-protein kinase C-MEK-ERK pathway is essential for KSHV infection, we have recently shown that KSHV also activates JNK and p38 mitogen-activated protein kinase (MAPK) pathways during primary infection (J. Xie, H. Y. Pan, S. Yoo, and S.-J. Gao, J. Virol. 79:15027-15037, 2005). Here, we found that activation of both JNK and p38 pathways was also essential for KSHV infection. Inhibitors of all three MAPK pathways reduced KSHV infectivity in both human umbilical vein endothelial cells (HUVEC) and 293 cells. These inhibitory effects were dose dependent and occurred at the virus entry stage of infection. Consistently, inhibition of all three MAPK pathways with dominant-negative constructs reduced KSHV infectivity whereas activation of the ERK pathway but not the JNK and p38 pathways enhanced KSHV infectivity. Importantly, inhibition of all three MAPK pathways also reduced the yield of infectious virions during KSHV productive infection of HUVEC. While the reduction of infectious virions was in part due to the reduced infectivity, it was also the result of direct modulation of KSHV lytic replication by the MAPK pathways. Accordingly, KSHV upregulated the expression of RTA (Orf50), a master transactivator of KSHV lytic replication, and activated its promoter during primary infection. Furthermore, KSHV activation of RTA promoter during primary infection was modulated by all three MAPK pathways, predominantly through their downstream target AP-1. Together, these results indicate that, by modulating multiple MAPK pathways, KSHV manipulates the host cells to facilitate its entry into the cells and postentry productive lytic replication during primary infection.
Immunogenicity and efficacy testing in chimpanzees of an oral hepatitis B vaccine based on live recombinant adenovirus. (1989)

As a major cause of acute and chronic liver disease as well as hepatocellular carcinoma, hepatitis B virus (HBV) continues to pose significant health problems world-wide. Recombinant hepatitis B vaccines based on adenovirus vectors have been developed to address global needs for effective control of hepatitis B infection. Although considerable progress has been made in the construction of recombinant adenoviruses that express large amounts of HBV gene products, preclinical immunogenicity and efficacy testing of candidate vaccines has remained difficult due to the lack of a suitable animal model. We demonstrate here that chimpanzees are susceptible to enteric infection by human adenoviruses type 7 (Ad7) and type 4 (Ad4) following oral administration of live virus. Moreover, after sequential oral immunization with Ad7- and Ad4-vectored vaccines containing the hepatitis B surface antigen (HBsAg) gene, significant antibody responses to HBsAg (anti-HBs) were induced in two chimpanzees. After challenge with heterologous HBV, one chimpanzee was protected from acute hepatitis and the other chimpanzee experienced modified HBV-induced disease. These data demonstrate the feasibility of using orally administered recombinant adenoviruses as a general approach to vaccination.
Quantitative detection of hepatitis B virus DNA in serum by a new rapid real‐time fluorescence PCR assay (2001)

A sensitive and accurate HBV DNA quantification assay is essential for monitoring hepatitis B virus (HBV) replication. This study evaluated a real-time PCR method performed in the LightCycler analyser for quantitative HBV DNA assay. HBV DNA results with this method were compared with those obtained using a branched-chain DNA (bDNA) solution hybridization assay. Real-time PCR was performed using two adjacent fluorescently labelled probes and primers corresponding to the HBV core gene. The same standard employed in the bDNA assay was used for calibration. Serum samples came from 193 HBV surface antigen (HBsAg)-positive patients (34 HBV e antigen (HBeAg)-positive and 93 with antibody to HBeAg (anti-HBe)), and 66 asymptomatic HBV carriers. In addition, we analysed serum samples from 8 anti-HBe-positive patients who had been receiving lamivudine treatment for more than three years. A linear standard curve was seen in the range from 10(3) to 10(8) copies/mL. In the reproducibility analysis, intra-assay coefficient of variation (CVs) at two known HBV DNA concentrations were 4% and 2% and interassay CVs were 6% and 4%. The median of serum HBV DNA by real-time PCR was 9.2 x 10(8) copies/mL in HBeAg-positive patients with persistently elevated alanine aminotransferase (ALT) levels, 1.3 x 10(7) copies/mL in anti-HBe-positive cases with persistently elevated ALT levels, 3.7 x 10(4) copies/mL in anti-HBe-positive patients with fluctuating ALT levels and 10(4) copies/mL in asymptomatic HBV carriers. The differences in HBV DNA levels among the various groups studied were statistically significant (P < 0.05). The cut-off between chronic hepatitis patients and asymptomatic carriers was found to be at a serum HBV DNA concentration of 5 x 10(4) copies/mL. Of the 109 serum samples with a viral load < 7.5 x 10(5) (negative by bDNA assay) 44 (40%) were positive by real-time PCR: 24 (56%) chronic hepatitis and 20 (33%) asymptomatic carriers. There was a positive association between HBV DNA levels determined by real-time PCR and ALT levels (P < 0.05), which was not observed with the bDNA assay for HBV DNA quantification. At 12 months of lamivudine treatment, 6 patients (75%) showed HBV DNA levels < 5 x 10(4) copies/mL (range < 10(3)-2 x 10(3)), significantly lower than at baseline. At 36 months, 2 of 8 (25%) showed HBV DNA levels persistently lower than 5 x 10(4) copies/mL (1.7 x 10(3), 6 x 10(3)). The LightCycler quantitative real-time PCR is a practical, sensitive, reproducible single-tube assay with a wide dynamic range of detection. The assay is automatic except for DNA extraction and the running time is only 70 min. The LightCycler real-time PCR is useful for identifying different states of HBV infection and for evaluating the efficacy of viral therapy.
Drug/substance reversal effects of a novel tri‐substituted benzoflavone moiety (BZF) isolated from Passiflora incarnata Linn.–a brief perspective (2003)

The present work is a mini-review of the author's original work on the plant Passiflora incarnata Linn., which is used in several parts of the world as a traditional medicine for the management of anxiety, insomnia, epilepsy and morphine addiction. A tri-substituted benzoflavone moiety (BZF) has been isolated from the bioactive methanol extract of this plant, which has been proposed in the author's earlier work to be responsible for the biological activities of this plant. The BZF moiety has exhibited significantly encouraging results in the reversal of tolerance and dependence of several addiction-prone psychotropic drugs, including morphine, nicotine, ethanol, diazepam and delta-9-tetrahydrocannabinol, during earlier pharmacological studies conducted by the author. In addition to this, the BZF moiety has exhibited aphrodisiac, libido-enhancing and virility-enhancing properties in 2-year-old male rats. When administered concomitantly with nicotine, ethanol and delta-9-tetrahydrocannabinol for 30 days in male rats, the BZF also prevented the drug-induced decline in sexuality in male rats. Because the BZF moiety isolated from P. incarnata is a tri-substituted derivative of alpha-naphthoflavone (7,8-benzoflavone), a well-known aromatase-enzyme inhibitor, the mode of action of BZF has been postulated to be a neurosteroidal mechanism vide in which the BZF moiety prevents the metabolic degradation of testosterone and upregulates blood - testosterone levels in the body. As several flavonoids (e.g. chrysin, apigenin) and other phytoconstituents also possess aromatase-inhibiting properties, and the IC50 value of such phytomoieties is the main factor determining their biochemical efficacy, by altering their chemical structures to attain a desirable IC50 value new insights in medical therapeutics can be attained, keeping in view the menace of drug abuse worldwide.
Orthogonalization of correlated Gaussian signals for Volterra system identification (1995)

This article presents a simple method for orthogonalizing correlated Gaussian input signals for identification of truncated Volterra systems of arbitrary order of nonlinearity P and memory length N. The procedure requires a Gram-Schmidt orthogonalizer for a vector containing N elements and some nonlinear processing of the output elements of the Gram-Schmidt processor. However, the nonlinear processors do not depend on the statistics of the input signals and, consequently, are easy to design and implement.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Etiology and disease process of benign prostatic hyperplasia (1989)

The natural history of benign prostatic hyperplasia (BPH) involves two phases. The first, or pathological phase of BPH, involves two stages, termed microscopic and macroscopic BPH, neither of which produces symptomatic clinical dysuria. Nearly all men throughout the world will eventually develop microscopic BPH if they live long enough. In only about one-half of the men with microscopic BPH, however, will microscopic BPH grow to produce a macroscopic enlargement of the gland (i.e., macroscopic BPH), suggesting that additional factors are required for the progression of microscopic to macroscopic BPH. Several theories have been proposed to explain the etiology of the pathological phase of BPH. The major theories include the hypotheses that pathological BPH is due to 1) a shift in prostatic androgen metabolism that occurs with aging, which leads to an abnormal accumulation of dihydrotestosterone, thus producing the enlarged prostate (i.e., DHT hypothesis), 2) a change in the prostatic stromal-epithelial interact that occurs with aging, which leads to an inductive effect on prostatic growth (i.e., embryonic reawakening theory), or 3) an increase in the total prostatic stem cell number and/or an increase in the clonal expanding of the stem cells into amplifying and transit cells that occurs with aging (i.e., stem cell theory). The second, or clinical phase of BPH, involves the progression of pathologic BPH to clinical BPH in which the patient develops symptomatic dysuria. Only about one-half the men with macroscopic BPH progress to clinical BPH. Although the macroscopic enlargement of the prostate is a necessary condition for the development of clinical BPH, this enlargement is usually not sufficient by itself for the progression of pathologic BPH to clinical BPH. The etiology of the progression of pathological BPH to clinical BPH requires additional factors (e.g., prostatitis, vascular infarct, tensile strength of the glandular capsule, etc.). A successful treatment for clinical BPH, therefore, does not necessarily require either the prevention or elimination of all degrees of pathologic BPH. Instead, what is needed is a therapy to prevent or reverse the progression of pathologic BPH to the clinical disease.
외국인 투자 유치에 있어서 지방정부의 역할 : 일본 자동차기업의 미국 현지 공장 설립 사례를 중심으로 (2001)

본 연구는 외국인 투자 유치를 위한 지방정부의 역할을 일본 자동차기업 유치 경쟁에 참여했던 미국 州정부의 사례를 통해 분석하여, IMF 이후 우리 나라 지방자치 단체들 사이에 가열되는 외자 유치 경쟁에 도움이 되는 정책적 시사점을 발견하려는 목적 아래 진행되었다. 1980년대 미국에 투자하였던 6개의 일본 자동차기업들의 입지 결정에 영향을 주었던 요인들을 분석하기 위해 로지스틱 회귀모델과 尤度率시험(likelihood ratio test) 방법을 사용하였다. 로지스틱 회귀분석 결과 州間 고속도로 연장, 투자업무 관련 예산 배정액, 해외사무소 數는 일본 자동차공장 입지 결정에 긍정적 영향을 미친 것으로 나타났으나, 세제 인센티브는 부정적 요인으로 나타났다. 특히, 예산 배정이나 해외 사무소 개설은 지방정부의 적극적인 투자 유인 정책이 외국인 투자를 유치하는데 도움이 되는 것으로 나타났다. 尤度率시험 결과에 따르면, 일본 자동차공장을 설립하려는 일본 기업은 미국 어느 州에 다른 일본 자동차공장이 이미 소재하고 있다는 사실에 의해 영향을 받는 것으로 나타났다. 이것은 비록 어느 주가 자동차산업에 우호적인 입지 조건을 갖추었다 하더라도, 만약 다른 일본 자동차공장이 그 주에 이미 입주해 있다면 새로운 공장을 유치 하기가 어렵다는 점을 밝혀주고 있다.
Distributed Sensor Networks. (1983)

Abstract : This report summarizes Distributed Sensor Networks research conducted during the period 1 April through 30 September 1978. One specific model for function decomposition and distribution is presented. A top level design of a strawman DSN for detecting and tracking low flying aircraft is described. High resolution acoustic signal processing algorithms for the strawman are specified and sized. Additional features of a multisite target search algorithm are presented. A moderately detailed model for simulation of an acoustic node under various scenarios is developed. New model simulation and experimental data analysis software are described and demonstrated. Technical issues involved with and plans for a digital acoustic data acquisition system are presented.
Allosterically Controllable Maxizyme-Mediated Suppression of Progression of Leukemia in Mice (2001)

Chronic myelogenous leukemia (CML) is a hematopoietic malignant disease associated with expression of a chimeric BCR-ABL gene. We recently succeeded in designing a novel allosterically controllable ribozyme, the maxizyme (Tanabe et al. Biomacromolecules 2000, 1, 108-117; Kuwabara et al. Biomacromolecules 2001, 2, 788-799), that not only specifically cleaves BCR-ABL mRNA and induces apoptosis in cultured CML cells but also shows significant inhibition against the growth of an established BV173 cell line in a mouse model (Tanabe et al. Nature 2000, 406, 473-474). As an extension of our studies, we tested the maxizyme against primary CML cells in the same mouse model. The maxizyme under the control of a tRNA(Val) promoter showed significant inhibition against the growth of the primary bone marrow cells from a Japanese patient with CML. Specifically, to examine the applicability of the maxizyme in the treatment of CML, we assessed the antitumor effect of the maxizyme in murine models of CML. Fourteen weeks after the injection of primary CML cells into a NOD-SCID mouse, the bone marrow of the mouse was filled with primary CML cells as a result of diffuse leukemia. In marked contrast, when maxizyme-expressing primary CML cells were injected, the mouse remained disease-free. These results further strengthen our earlier suggestion that the maxizyme technology might provide a useful approach to the treatment of CML.
Was There an Epidemic of Diabetes in Nonwhite Adolescents in Allegheny County, Pennsylvania? (1998)

For the first time in the Allegheny County registry, and in any other registry, nonwhites showed a higher incidence of IDDM than whites. The high incidence in the 15-19 years age-group was responsible for this phenomenon. This epidemic of diabetes in adolescent nonwhites may be the result of a rising incidence of classical IDDM or another type of diabetes. Further studies using population-based registries are needed to determine whether this increase is being seen in other areas and other ethnic groups and to clarify the reasons for the increase in IDDM among blacks.
Bifacial Nucleoside as a Surrogate for Both T and A in Duplex DNA (2011)

A new functional bifacial nucleoside derived from 7-aminopyrimido[4,5-d]pyrimidine-2,4(1H,3H)-dione, a Janus-type nucleobase, has been synthesized and incorporated into DNA oligonucleotides. The nucleobase, having self-complementary H-bonding faces, mimics both T and A and engages in the corresponding Watson-Crick-like base pairs, forming stable duplexes.
Effect of glycosylation of recombinant human granulocytic colony-stimulating factor on expansion cultures of umbilical cord blood CD34+ cells. (1999)

Our results suggest that the stability of the G-CSF molecule has a predominant effect on the higher biological activity found. A glycosylated form of G-CSF is recommended for in vitro cultures using serum-dependent conditions.
Enhanced Oleic Acid Content in the Soybean Mutant M23 Is Associated with the Deletion in the Fad2‐1a Gene Encoding a Fatty Acid Desaturase (2007)

Abstract Oleic acid is one of the three major unsaturated fatty acids in soybean oil. Expression of the embryo‐specific Fad2‐1 gene correlates with fatty acid biosynthesis and oil deposition in developing seeds. Elevated levels of oleate in the X‐ray‐induced mutant line M23 have been shown to be associated with the deletion of a Fad2‐1 gene. In soybean, two homologs of the Fad2‐1 gene, termed Fad2‐1a (L43920) and Fad2‐1b (AY611472), presumably encode functional embryo‐specific fatty acid desaturase. The objectives of this investigation were to determine which copy of the Fad2‐1 gene is associated with the increased oleate content in the mutant line and what is the relative transcript abundance of these two embryo‐specific genes. PCR and DNA blot analyses showed that increased oleate content in M23 mutant was associated with the deletion of Fad2‐1a . These results were further validated using five independent soybean populations developed by crossing mid‐oleate and normal‐oleate parents. Investigation of the soybean expressed sequence tag database and reverse transcription PCR analyses revealed that Fad2‐1b is the predominantly transcribed copy of the Fad2‐1 gene. We hypothesize that null mutation in Fad2‐1b in the fad2‐1a mutant background should further elevate the oleic contents of soybean oil.