Miracle-dz/UniFAR-FTUs huggingface dataset:
Involving Tyrosine Kinase Signaling Expressing High-Affinity Nerve Growth Factor Binding Sites Cancer Cell Lines and a Human Glioblastoma Cell Line Nerve Growth Factor Stimulates Clonal Growth of Human Lung

The growth of a panel of 22 different human tumor, leukemia, and lymphoma cell lines was examined in a human tumor cloning assay in agar or methylcellulose and a tritiated thymidine uptake assay. The cultures were performed in the absence or presence of increasing concentrations (0.5-500 ng/ml) of nerve growth factor (NGF). The growth of 17 of the 22 cell lines was not significantly and reproducibly affected by NGF. There was minor (1.2-fold) but reproducible stimulation of clonal growth in one glioblastoma cell line (86-HG-39) by NGF, but in this cell line NGF induced no growth modulation in a tritiated thymidine uptake assay. However, clonal growth of another glioblastoma cell line (87-HG-31) and all three lung cancer cell lines tested (HTB 119, HTB 120, CCL 185) could be stimulated up to 3-fold by NGF with a dose-response relationship for the growth factor. Growth stimulation by NGF could be completely reversed by neutralizing anti-NGF antibody and by the tyrosine kinase inhibitor genistein. Evaluation of secondary plating efficiency revealed the stimulation of colony formation as representing self-renewal and not terminal differentiation. Reverse transcriptase-PCR experiments in the five responding cell lines showed expression of both low-affinity NGF receptor (glycoprotein 75) and c-trk transcripts on the mRNA level. Of the five responding cell lines, only 86-HG-39, the cell line with the lowest responsiveness, revealed low-affinity NGF receptor on the protein level; the other four cell lines with high responsiveness, including the three lung cancer cell lines, expressed no low-affinity NGF receptor as shown by fluorescence-activated cell sorter analysis and immunoprecipitation using the ME 20.4 antibody. Immunoprecipitation using anti-fri antibodies was negative in all five responding ceil lines. However, binding studies with iodinated NGF showed only low-affinity binding on the 86-HG-39 cell line and only high-affinity binding on the high-responder cell lines CCL 185 and 87-HG-31. In summary, our data suggest that NGF can be operative in stimulation of clonal growth of malignant tumor cells. High-affinity but not low-affinity binding sites mediate signal transduction for clonal growth and signaling involves tyrosine kinase activity.
An Analysis of Diagnostic Reasoning 11 . The Strategy of Intermediate Decisions '

The process of diagnostic reasoning contains a sequence of intellectual "stations" through which a patient's manifestations are transferred en route to the diagnostic entities that emerge as explanatory conclusions. The previous paper of this series (1) contained an account of the domains, disorders, derangements, and other entities that act as "stations" during the directional sequence of the reasoning. In this paper, I shall try to indicate the way in which the transfers through these "stations" are effected by a rational series of intermediate decisions that are commonly subsumed under the name of judgment.
The Humoral Immune Response to HCV: Understanding is Key to Vaccine Development

Hepatitis C virus (HCV) remains a global problem, despite advances in treatment. The low cost and high benefit of vaccines have made them the backbone of modern public health strategies, and the fight against HCV will not be won without an effective vaccine. Achievement of this goal will benefit from a robust understanding of virus–host interactions and protective immunity in HCV infection. In this review, we summarize recent findings on HCV-specific antibody responses associated with chronic and spontaneously resolving human infection. In addition, we discuss specific epitopes within HCV’s envelope glycoproteins that are targeted by neutralizing antibodies. Understanding what prompts or prevents a successful immune response leading to viral clearance or persistence is essential to designing a successful vaccine.
Basement membrane proteoglycan in various tissues: characterization using monoclonal antibodies to the Engelbreth-Holm-Swarm mouse tumor low density heparan sulfate proteoglycan

The Engelbreth-Holm-Swarm mouse tumor has been found to produce at least two molecular species of heparan sulfate proteoglycan, a low density one (LD) and a high density one, which differ not only in core proteins but also in glycosaminoglycan structures (Kato, M., Y. Koike, Y. Ito, S. Suzuki, and K. Kimata. 1987. J. Biol. Chem. 262:7180-7188). With aim at investigating their distribution and possible functions in tissues, monoclonal antibodies were produced. Hybridomas obtained by fusion of NS-1 mouse myeloma cells with spleen cells from the rat immunized with a mixture of these proteoglycans were selected by their ability to react with the antigen. Two of them secreted monoclonal antibodies (IgG2a), designated HK-84 and HK-102, that recognize specifically the core protein moiety of LD. Immunofluorescent staining of various tissues (skeletal muscle, cardiac muscle, lung, brain, and kidney) with these monoclonal antibodies has demonstrated that the antigen molecules were present in all basement membranes of these tissues. SDS-PAGE of heparitinase-treated proteoglycan fractions prepared from these tissues and subsequent immunoblotting using these monoclonal antibodies have confirmed that the antigen molecule was LD, and further suggested that there was a tissue-specific variation in the core molecular size. Based on these results, we propose that LD may be an essential component in all basement membranes.
Post-Crackdown Effectiveness of Field-Based Forest Law Enforcement in the Brazilian Amazon

Regulatory enforcement of forest conservation laws is often dismissed as an ineffective approach to reducing tropical forest loss. Yet, effective enforcement is often a precondition for alternative conservation measures, such as payments for environmental services, to achieve desired outcomes. Fair and efficient policies to reducing emissions from deforestation and forest degradation (REDD) will thus crucially depend on understanding the determinants and requirements of enforcement effectiveness. Among potential REDD candidate countries, Brazil is considered to possess the most advanced deforestation monitoring and enforcement infrastructure. This study explores a unique dataset of over 15 thousand point coordinates of enforcement missions in the Brazilian Amazon during 2009 and 2010, after major reductions of deforestation in the region. We study whether local deforestation patterns have been affected by field-based enforcement and to what extent these effects vary across administrative boundaries. Spatial matching and regression techniques are applied at different spatial resolutions. We find that field-based enforcement operations have not been universally effective in deterring deforestation during our observation period. Inspections have been most effective in reducing large-scale deforestation in the states of Mato Grosso and Pará, where average conservation effects were 4.0 and 9.9 hectares per inspection, respectively. Despite regional and actor-specific heterogeneity in inspection effectiveness, field-based law enforcement is highly cost-effective on average and might be enhanced by closer collaboration between national and state-level authorities.
Mutations in CCDC39 and CCDC40 are the Major Cause of Primary Ciliary Dyskinesia with Axonemal Disorganization and Absent Inner Dynein Arms

Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder caused by cilia and sperm dysmotility. About 12% of cases show perturbed 9+2 microtubule cilia structure and inner dynein arm (IDA) loss, historically termed “radial spoke defect. ” We sequenced CCDC39 and CCDC40 in 54 “radial spoke defect” families, as these are the two genes identified so far to cause this defect. We discovered biallelic mutations in a remarkable 69% (37/54) of families, including identification of 25 (19 novel) mutant alleles (12 in CCDC39 and 13 in CCDC40). All the mutations were nonsense, splice, and frameshift predicting early protein truncation, which suggests this defect is caused by “null” alleles conferring complete protein loss. Most families (73%; 27/37) had homozygous mutations, including families from outbred populations. A major putative hotspot mutation was identified, CCDC40 c.248delC, as well as several other possible hotspot mutations. Together, these findings highlight the key role of CCDC39 and CCDC40 in PCD with axonemal disorganization and IDA loss, and these genes represent major candidates for genetic testing in families affected by this ciliary phenotype. We show that radial spoke structures are largely intact in these patients and propose this ciliary ultrastructural abnormality be referred to as “IDA and microtubular disorganisation defect,” rather than “radial spoke defect. ”
Changes in antioxidant systems in sunflower partial resistant and susceptible lines as affected by Sclerotinia sclerotiorum

Sunflower, Helianthus annuus L. , is a major oil-seed crop widely cultivated throughout the globe. White mold, caused by necrotrophic pathogen Sclerotinia sclerotiorum (Lib.) de Bary, is a common and widespread disease of sunflower. Changes in various physiological activities such as production of malondialdehyde (MDA) as the main end product of lipid peroxidation, enzymatic and non-enzymatic activities and proline content, were investigated in leaves and stems of sunflower lines either resistant or susceptible to S. sclerotiorum. The results showed accumulation of high amount of free proline in the leaves of the resistant line. S. sclerotiorum invasion resulted in increase in the MDA content in both lines compared to the controls. Superoxide dismutase, ascorbate peroxidase and guaiacol peroxidase activities significantly increased in the stem and leaves of inoculated lines. In the resistant line, Sclerotinia infection significantly induced catalase (CAT) activity both in the stem and leaves of contaminated plants. The activity of CAT was significantly decreased in susceptible line. Based on our results the activity of antioxidant enzymes was much pronounced in sunflower resistant line than in susceptible one. Studied lines showed distinctive activity considering different biochemical parameters, which may point to further directions in exploring host-pathogen interaction and lead to selection and production of new lines to achieve an improvement of plant adaptation to pathogen.
Quadratic Convergence of a Nonsmooth Newton-Type Method for Semidefinite Programs Without Strict Complementarity

We consider a Newton-type method for the solution of semidefinite programs. This Newton-type method is based on a semismooth reformulation of the semidefinite program as a nonsmooth system of equations. We establish local quadratic convergence of this method under a linear independence assumption and a weak nondegeneracy condition that implies uniqueness of the optimal solution but does not imply strict complementarity.
Glutathione peroxidase induced in rat retinas to counteract photic injury.

PURPOSE To examine the hypothesis that glutathione peroxidase (GPX) is induced at different time points after retinal exposure to light and localizes in different retinal cells. METHODS The rats were kept in cyclic light for 2 weeks before the experiments. The animals were maintained in 12-hour light-dark cycles, before and after exposure to intense white fluorescent light, for as long as 24 hours and then returned to cyclic light. Expression of GPX was measured by immunohistocytochemistry and Western and Northern blot analyses. Light-induced retinal damage was determined by the thickness of the outer nuclear layer (ONL) thickness in relation to total retinal thickness. RESULTS GPX labeling did not appear in the photoreceptor inner segments, and slight labeling was observed in the photoreceptor outer segments or the retinal pigment epithelial (RPE) cells in the normal retina kept in cyclic light. In retinal specimens maintained in light for 12 and 24 hours, GPX labeling was induced in the photoreceptor outer segments and RPE cells. High expression of GPX in the RPE was sustained until day 7 after challenge. In contrast, GPX expression in the photoreceptor outer segments decreased on day 1 and disappeared on days 3 and 7 after exposure. Intense GPX labeling was seen from the internal limiting membrane to the ganglion cell layer. GPX labeling was constantly localized in both high-intensity white light and cyclic conditions, suggesting no induction of GPX in those areas. In addition, GPX labeling was apparent at the posterior retinal pole but not at the peripheral retina. We observed marked upregulation of GPX mRNA in rats kept in high-intensity white light. One, 3, and 7 days after exposure to high-intensity white light, there was a significant difference (P < 0.0001) between the control and experimental groups in the ratio of the outer nuclear layer thickness to the entire retina. CONCLUSIONS GPX was induced at different time points after exposure to high-intensity white light and localized in different retinal cells. Changes in expression of GPX after exposure to light may be related to the difference in susceptibility of the retina to damage by light.
Effect of Outdoor Sport Motivation on Sport Adherence in Adolescents—The Mediating Mechanism of Sport Atmosphere

In view of the important effect of outdoor sports on the education and development in adolescents,the adherence to outdoor sports attracts more and more attention.Using exploratory factor analysis(EFA) and confirmatory factor analysis(CFA),the validity and reliability of the "Outdoor Sport Motivation Scale for adolescents","Outdoor Sport Atmosphere Scale for adolescents",and "Outdoor Sport Adherence Scale for adolescents" were examined;then stepwise regression analysis was conducted to examine the mediating effect of sport atmosphere between sport motivation and sport adherence.The results revealed that the data for the three scales were represented appropriately by the hypothesized model,and sport atmosphere played partly mediating mechanism between sport motivation and sport adherence.
A defunctioning polymorphism in FCGR2B is associated with protection against malaria but susceptibility to systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease more prevalent in people of African and Asian origin than Caucasian origin. FcγRIIb is an inhibitory Fc receptor with a critical role in immune regulation. Mouse data suggest that FcγRIIb deficiency increases susceptibility to autoimmune disease but protects against infection. We show that a SNP in human FCGR2B that abrogates receptor function is strongly associated with susceptibility to SLE in both Caucasians and Southeast Asians. The minor allele of this SNP is more common in Southeast Asians and Africans, populations from areas where malaria is endemic, than in Caucasians. We show that homozygosity for the minor allele is associated with substantial protection against severe malaria in an East African population (odds ratio = 0.56; P = 7.1 × 10−5). This protective effect against malaria may contribute to the higher frequency of this SNP and hence, SLE in Africans and Southeast Asians.
B WIRELESS NETWORKS MAC LAYER DIAGNOSTIC CONTROLLER IN MOBILE AD HOC NETWORK

In a mobile ad hoc network (MANET), when a node fails during the RTS-CTS handshake process, the MAC protocol is able to identify whether the failure was caused by link failure or due to congestion by inspecting the recorded radio signal strengths. If the cause is due to actual link failure, then MAC abandons any further attempt to retry communicating with the node. If the failure is due to congestion, the conventional approach in attempt to reconnect the link is wasteful of both time and bandwidth. This will in turn cause packet loss and hence degradation in the TCP performance. In this paper, an intelligent link diagnostic controller for IEEE 802.11b wireless network is proposed. The proposed mechanism incorporates fuzzy controller in the MAC protocol of a node to diagnose the link based on the distances and relative velocities before the attempt to reconnect is made. The incorporated intelligence allows a node to adjust the number of retry in proportional to the probability of getting the node connected. Simulation results show that the proposed fuzzy approach increases the amount of TCP packets transferred whilst reducing the number of TCP packets dropped and maintaining the level of overhead traffic. This mechanism improves the TCP performance by7% on average.
AM-demodulation of speech spectra and its application io noise robust speech recognition

In this paper, a novel algorithm that resembles amplitude demodulation in the frequency domain is introduced, and its application to automatic speech recognition (ASR) is studied. Speech production can be regarded as a result of amplitude modulation (AM) with the source (excitation) spectrum being the carrier and the vocal tract transfer function (VTTF) being the modulating signal. From this point of view, the VTTF can be recovered by amplitude demodulation. Amplitude demodulation of the speech spectrum is achieved by a novel nonlinear technique, which effectively performs envelope detection by using amplitudes of the harmonics and discarding inter-harmonic valleys. The technique is noise robust since frequency bands of low energy are discarded. The same principle is used to reshape the detected envelope. The algorithm is then used to construct an ASR feature extraction module. It is shown that this technique achieves superior performance to MFCCs in the presence of additive noise. Recognition accuracy is further improved if peak isolation [1] is also performed.
PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena

Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing that the only abundant bias pattern is for asparagine bias with subsidiary serine bias. We anticipate that this database will be a useful experimental aid and reference resource. It is freely available at: http://libaio.biol.mcgill.ca/prion.
Computerized Tailored Interventions to Enhance Prevention and Screening for Hepatitis C Virus Among People Who Inject Drugs: Protocol for a Randomized Pilot Study

Background Hepatitis C virus (HCV) infection is a growing problem among people who inject drugs. Strategies to reduce disease transmission (eg, syringe exchange programs) and facilitate HCV screening and linkage are available but are under-utilized in many communities affected by injection drug use. Novel approaches to increasing the use of these strategies are needed. Objective The goals of this project are to (1) develop and pilot test a computerized tailored intervention for increasing HCV screening and decreasing risky drug use behavior among people who inject drugs and (2) determine the feasibility of disseminating such an intervention using peer-based referrals in the setting of a community-based syringe exchange program. Methods This 2-arm, randomized pilot study is being conducted in a large-volume, multisite syringe exchange program in southern Wisconsin. A social network–based strategy was used to recruit a total of 235 adults who reported past-month injection of opioids, cocaine, or methamphetamine. Network recruiters were identified among clients requesting services from the syringe exchange program and were enlisted to refer eligible peers to the study. All participants completed a computer-adapted questionnaire eliciting information about risk behaviors and their knowledge, attitudes, and prior experiences related to HCV screening. Subjects were then randomly assigned to receive usual care, consisting of standard counseling by syringe exchange staff, or the Hep-Net intervention, which provides algorithm-based, real-time tailored feedback and recommendations for behavior change in the style of motivational interviewing. Changes in drug use behaviors and attitudes will be assessed during a second session between 90 and 180 days after the baseline visit. Frequency of repeat HCV testing and HCV incidence will be assessed through a database search 1 year after study completion. Results Recruitment for this study was completed in April 2015. Follow-up of enrolled participants is expected to continue until March 2016. Network recruiters were enrolled who referred a total of 195 eligible peers (overall N=235). At baseline, the median age was 34 years; 41.3% (97/235) were non-white; and 86.4% (203/235) reported predominantly injecting heroin. Most participants (161/234, 68.8%) reported sharing injection equipment in the past and of these, 30.4% (49/161) had never been tested for HCV. Conclusions This study will provide preliminary evidence to determine whether incorporating computerized behavioral interventions into existing prevention services at syringe exchange programs can lead to adoption of healthier behaviors. Trial Registration ClinicalTrials.gov NCT02474043; https://clinicaltrials.gov/ct2/show/NCT02474043 (Archived by WebCite at http://www.webcitation.org/6dbjUQG7J)
The Parzen kernel approach to learning in non-stationary environment

In this paper a method for nonparametric regression estimation in non-stationary environment is presented. The Parzen kernels are used to design the recursive general regression neural networks to track changes of non-stationary system under non-stationary noise. The probabilistic properties of the proposed method are investigated. Experimental results are presented and discussed.