tbuckley/cabot-search huggingface dataset:
Decoding Neural Representational Spaces Using Multivariate Pattern Analysis
Authors: James V. Haxby, Andrew C. Connolly, J. Swaroop Guntupalli
Journal: Annual Review of Neuroscience (2014)

A major challenge for systems neuroscience is to break the neural code. Computational algorithms for encoding information into neural activity and extracting information from measured activity afford understanding of how percepts, memories, thought, and knowledge are represented in patterns of brain activity. The past decade and a half has seen significant advances in the development of methods for decoding human neural activity, such as multivariate pattern classification, representational similarity analysis, hyperalignment, and stimulus-model-based encoding and decoding. This article reviews these advances and integrates neural decoding methods into a common framework organized around the concept of high-dimensional representational spaces.
FDG-PET/CT Imaging Predicts Histopathologic Treatment Responses after the Initial Cycle of Neoadjuvant Chemotherapy in High-Grade Soft-Tissue Sarcomas
Authors: Matthias R. Benz, Johannes Czernin, Martin S. Allen-Auerbach, William D. Tap, Sarah M. Dry, David Elashoff, Kira Chow, Vladimir Evilevitch, Jeff J. Eckardt, Michael E. Phelps, Wolfgang A. Weber, Fritz C. Eilber
Journal: Clinical Cancer Research (2009)

Abstract Purpose: In patients with soft-tissue sarcoma (STS), the early assessment of treatment responses is important. Using positron emission tomography/computed tomography (PET/CT) with [18F]fluorodeoxyglucose (FDG), we determined whether changes in tumor FDG uptake predict histopathologic treatment responses in high-grade STS after the initial cycle of neoadjuvant chemotherapy. Experimental Design: From February 2006 to March 2008, 50 patients with resectable high-grade STS scheduled for neoadjuvant therapy and subsequent tumor resection were enrolled prospectively. FDG-PET/CT before (baseline), after the first cycle (early follow-up), and after completion of neoadjuvant therapy (late follow-up) was done. Tumor FDG uptake and changes were measured by standardized uptake values. Histopathologic examination of the resected specimen provided an assessment of treatment response. Patients with ≥95% pathologic necrosis were classified as treatment responders. FDG-PET/CT results were compared with histopathologic findings. Results: At early follow-up, FDG uptake decreased significantly more in 8 (16%) responders than in the 42 (84%) nonresponders (−55% versus −23%; P = 0.002). All responders and 14 of 42 nonresponders had a ≥35% reduction in standardized uptake value between baseline and early follow-up. Using a ≥35% reduction in FDG uptake as early metabolic response threshold resulted in a sensitivity and specificity of FDG-PET for histopathologic response of 100% and 67%, respectively. Applying a higher threshold at late follow-up improved specificity but not sensitivity. CT had no value at response prediction. Conclusion: A 35% reduction in tumor FDG uptake at early follow-up is a sensitive predictor of histopathologic tumor response. Early treatment decisions such as discontinuation of chemotherapy in nonresponding patients could be based on FDG-PET criteria.
Risk of myocardial infarction and cardiovascular death associated with inhaled corticosteroids in COPD
Authors: Y. K. Loke, C. S. Kwok, S. Singh
Journal: European Respiratory Journal (2009)

The effect of long-term inhaled corticosteroid (ICS) use on myocardial infarction (MI) and cardiovascular (CV) death in chronic obstructive pulmonary disease (COPD) remains uncertain. We conducted a systematic search of MEDLINE, EMBASE, ISI, regulatory documents and manufacturers' trial registries for long-term (&gt;24 weeks duration) randomised controlled trials (RCTs) or controlled observational studies reporting on CV outcomes or death with ICS use in COPD. A fixed effects model was used to calculate the relative risks (RRs) and 95% CIs. 23 RCTs with 24–160 weeks of follow-up were included. In the RCTs, ICS were not associated with a significantly reduced risk of MI (RR 0.95, 95% CI 0.73–1.23; p = 0.68, I 2 = 0%), CV death (RR 1.02; 95% CI 0.81–1.27; p = 0.89, I 2 = 0%), or mortality (RR 0.96, 95% CI 0.86–1.07; p = 0.43, I 2 = 0%). In the observational studies, ICS use was associated with a significant reduction in CV death (two studies: RR 0.79, 95% CI 0.72–0, 86; p &lt;0.0001, I 2 = 44%) and mortality (11 studies: RR 0.78, 95% CI 0.75–0.80; p&lt;0.001, I 2 = 33%). Publication bias via funnel plot asymmetry was noted for mortality in the observational studies (Egger test, p = 0.05). We conclude that while observational studies suggest that ICS may potentially confer CV or mortality benefit, RCTs failed to show any significant effect of ICS therapy on MI or CV death. These conflicting findings need to be clarified through further research.
A phase II study of Tomudex alternated with methotrexate, 5-fluorouracil, leucovorin in first-line chemotherapy of metastatic colorectal cancer
Authors: S. Cascinu, R.R. Silva, R. Labianca, S. Barni, R. Mattioli, G. Martignoni, L. Frontini, G. Gasparini, V. Catalano, A.M. Baldelli, L. Giuliodori, R. Agostinelli, G. Catalano
Journal: Annals of Oncology (1999)
High rate of spontaneous viral clearance in a cohort of vertically infected hepatitis C virus infants: what lies behind?
Authors: Oronzo Ceci, Marcella Margiotta, Fiorino Marello, Ruggiero Francavilla, Enzo Lerardi, Pasquale Loizzi, Luigi Impedovo, Antonio Francavilla
Journal: Journal of Hepatology (2001)
Deficiency in mouse Y chromosome long arm gene complement is associated with sperm DNA damage
Authors: Yasuhiro Yamauchi, Jonathan M Riel, Zoia Stoytcheva, Paul S Burgoyne, Monika A Ward
Journal: Genome biology (2010)

Mice with severe non-PAR Y chromosome long arm (NPYq) deficiencies are infertile in vivo and in vitro. We have previously shown that sperm from these males, although having grossly malformed heads, were able to fertilize oocytes via intracytoplasmic sperm injection (ICSI) and yield live offspring. However, in continuing ICSI trials we noted a reduced efficiency when cryopreserved sperm were used and with epididymal sperm as compared to testicular sperm. In the present study we tested if NPYq deficiency is associated with sperm DNA damage - a known cause of poor ICSI success.We observed that epididymal sperm from mice with severe NPYq deficiency (that is, deletion of nine-tenths or the entire NPYq gene complement) are impaired in oocyte activation ability following ICSI and there is an increased incidence of oocyte arrest and paternal chromosome breaks. Comet assays revealed increased DNA damage in both epididymal and testicular sperm from these mice, with epididymal sperm more severely affected. In all mice the level of DNA damage was increased by freezing. Epididymal sperm from mice with severe NPYq deficiencies also suffered from impaired membrane integrity and abnormal chromatin condensation and suboptimal chromatin protamination. It is therefore likely that the increased DNA damage associated with NPYq deficiency is a consequence of disturbed chromatin remodeling.This study provides the first evidence of DNA damage in sperm from mice with NPYq deficiencies and indicates that NPYq-encoded gene/s may play a role in processes regulating chromatin remodeling and thus in maintaining DNA integrity in sperm.
The birth of clinical body plethysmography: it was a good week
Authors: John B. West
Journal: Journal of Clinical Investigation (2004)

Nearly fifty years ago, Arthur B. DuBois, Julius H. Comroe Jr., and their colleagues published two papers on the use of body plethysmography to measure lung volume and airway resistance. These two articles in the JCI are almost the most-cited doublet in the Journal’s entire archive. Remarkably, the methods described then are still in use today in clinical pulmonary function laboratories. Though body plethysmography had been used before, there were serious technical problems; it was extraordinary that DuBois managed to solve most of these in one week. Times have changed and molecular medicine now dominates the JCI, but these articles remind us that biomedical research goes beyond the molecular.
Processes to Activate Phase III Clinical Trials in a Cooperative Oncology Group: The Case of Cancer and Leukemia Group B
Authors: David M. Dilts, Alan B. Sandler, Matthew Baker, Steven K. Cheng, Stephen L. George, Kathleen S. Karas, Stephen McGuire, Gourija S. Menon, Jason Reusch, Debbie Sawyer, Maren Scoggins, Amy Wu, Kai Zhou, Richard L. Schilsky
Journal: Journal of Clinical Oncology (2006)

National Cancer Institute-sponsored cooperative oncology groups are major sponsors of phase III clinical trials, yet the time and steps required to design and activate such studies has not been well studied. We examine the processes and document the calendar time required to activate such studies opened by the Cancer and Leukemia Group B (CALGB).Setup steps were documented by (1) interviewing CALGB headquarters and statistical center staff and committee chairs to discover the steps required to transit from concept development to final study activation, (2) reviewing procedure manuals, and (3) inspecting all study records, documents, and e-mails to identify any additional steps. Calendar time was collected for each major process.Thirteen phase III studies were activated by CALGB during the study period of May 2002 to May 2005. More than 370 distinct processes were required for study activation: 317 work steps, 42 decision points, and 29 processing loops. Sixty-three percent of the decision points were outside CALGB. The complete process map measures 243.5" x 41" in 8-point font. Median calendar days to activate a phase III study at CALGB was 580 days (range, 295 to 1,248 days) from concept approval and 784 days (range, 537 to 1,130 days) from initial conception of the study.Setup of a phase III study at a major cooperative oncology group is a complex and lengthy process, with the majority of decision points external to the cooperative group. To improve the activation process, research should to be directed toward both internal and external groups and processes.
Retrotransposons and retroviruses: analysis of the envelope gene
Authors: E. Lerat, P. Capy
Journal: Molecular Biology and Evolution (1999)

Retroviruses and long terminal repeat (LTR) retrotransposons share a common structural organization. The main difference between these retroelements is the presence of a functional envelope (env) gene in retroviruses, which is absent or nonfunctional in LTR retrotransposons. Several similarities between these two groups of retroelements have been detected for the reverse transcriptase, gag, and integrase domains. Assuming that each of these domains shares a common ancestral sequence, several hypotheses could account for the emergence of retroviruses from LTR retrotransposons. In this context, the positions of elements such as gypsy and the members of the Ty3 subfamily are not clear, since they are classified as retroviruses but phylogenetically they are assigned to the LTR retrotransposon group. We compared the env gene products of these retroelements and identified two similar motifs in retroviruses and LTR retrotransposons. These two regions do not occur in the same order. If we assume that they are derived from the same ancestral sequence, this could result from independent acquisition of the various domains rather than the single acquisition of the whole env gene. However, we cannot exclude the possibility that the env gene was reorganized after being acquired. Trees based on these regions show that these two groups of elements are clearly distinguished. These trees are similar to those obtained from reverse transcriptase or integrase. In trees based on reverse transcriptase, the retroviruses with complete or partial env genes can be distinguished from the other LTR retrotransposons.
Popular Attitudes and Beliefs About Tranquilizers
Authors: DEAN I. MANHEIMER, SUSAN T. DAVIDSON, MITCHELL B. BALTER, GLEN D. MELLINGER, IRA H. CISIN, HUGH J. PARRY
Journal: American Journal of Psychiatry (1973)

In a nationwide survey of the extent and nature of psychotherapeutic drug use, respondents were also questioned about their knowledge of tranquilizers and their attitudes toward the use of these drugs in general and in specific situations. The survey revealed surprising similarities of attitudes across demographic subgroups. Although respondents believed in the efficacy of tranquilizers and were willing to condone their use in some specific circumstances, they also had doubts about their long-term effects and about the morality of using them. Doubts about the morality of using tranquilizers were associated with traditional stoic values.
Experience is no improvement over talent
Authors: Kurt A. Heller, Albert Ziegler
Journal: Behavioral and Brain Sciences (1998)

Our recapitulation of the work by Howe et al. is a clear approval of the passages in which the talent concept is critically questioned. On the other hand, Howe et al. must themselves come to terms with most of the accusations they place at the door of talent researchers. The evidence they present to support the experience concept is lacking with respect to current theoretical and methodological standards.
Relationship Between a High-Risk Haplotype in the<i>DTNBP1</i>(Dysbindin) Gene and Clinical Features of Schizophrenia
Authors: Ayman H. Fanous, Edwin J. van den Oord, Brien P. Riley, Steven H. Aggen, Michael C. Neale, F. Anthony O’Neill, Dermot Walsh, Kenneth S. Kendler
Journal: American Journal of Psychiatry (2005)

The purpose of this study was to determine whether a haplotype in the dystrobrevin binding protein 1 (DTNBP1) gene previously associated with schizophrenia not only increases the susceptibility to psychotic illness but also to a more or less clinically specific form of psychotic illness.In the Irish Study of High-Density Schizophrenia Families, subjects with psychotic illness (N=755) were given lifetime ratings of clinical features according to the Operational Criteria Checklist for Psychotic Illness. Exploratory and confirmatory factor analyses were used to extract five factors-hallucinations, delusions, negative, manic, and depressive symptoms-and to create factor-derived scores. The family-based transmission disequilibrium test operationalized in the program TRANSMIT was used to determine whether a high-risk haplotype in the DTNBP1 gene was overtransmitted to subjects in the upper 20th and 40th percentiles for each factor score. These results were compared to baseline overtransmission by examining the empirical distribution of chi-square statistics in groups of 5,000 replicates in which 20% and 40% of ill subjects were randomly selected. This analysis was done for both narrow and broad definitions of psychotic illness.Subjects in the upper 40th percentile for the negative symptom factor--in both the narrowly (p=0.004) and broadly (p=0.01) defined illness groups--were more likely to inherit the high-risk haplotype than would be expected by chance. No other significant relationships between clinical features and high-risk haplotype transmission were observed.The etiologically relevant variation in DTNBP1, which is in presumptive linkage disequilibrium with the high-risk haplotype, may predispose individuals to a form of psychotic illness associated with high levels of negative symptoms. This finding supports previous evidence suggesting that genetic factors influence the clinical heterogeneity of schizophrenia.
Recurrent Diabetic Ketoacidosis in Inner-City Minority Patients
Authors: Lori Randall, Jovan Begovic, Megan Hudson, Dawn Smiley, Limin Peng, Njalalia Pitre, Denise Umpierrez, Guillermo Umpierrez
Journal: Diabetes Care (2011)

To conduct a bedside study to determine the factors driving insulin noncompliance in inner-city patients with recurrent diabetic ketoacidosis (DKA).We analyzed socioeconomic and psychological factors in 164 adult patients with DKA who were admitted to Grady Hospital between July 2007 and August 2010, including demographics, diabetes treatment, education, and mental illness. The Patient Health Questionnaire-9 and the Short Form-36 surveys were used to screen for depression and assess quality of life.The average number of admissions was 4.5 ± 7 per patient. A total of 73 patients presented with first-time DKA, and 91 presented with recurrent DKA; 96% of patients were African American. Insulin discontinuation was the leading precipitating cause in 68% of patients; other causes were new-onset diabetes (10%), infection (15%), medical illness (4%), and undetermined causes (3%). Among those who stopped insulin, 32% gave no reasons for stopping, 27% reported lack of money to buy insulin, 19% felt sick, 15% were away from their supply, and 5% were stretching insulin. Compared with first-time DKA, those with recurrent episodes had longer duration of diabetes (P < 0.001), were a younger age at the onset of diabetes (P = 0.04), and had higher rates of depression (P = 0.04), alcohol (P = 0.047) and drug (P < 0.001) abuse, and homelessness (P = 0.005). There were no differences in quality-of-life scores, major psychiatric illnesses, or employment between groups.Poor adherence to insulin therapy is the leading cause of recurrent DKA in inner-city patients. Several behavioral, socioeconomic, psychosocial, and educational factors contribute to poor compliance. The recognition of such factors and the institution of culturally appropriate interventions and education programs might reduce DKA recurrence in minority populations.
Psychological stress and colitis
Authors: E A MAYER
Journal: Gut (2000)

Idiopathic inflammatory bowel disease is a chronic relapsing condition.The role of stress in causing relapses of inflammatory bowel disease remains controversial.We now show that colitis induced in mice by dinitrobenzenesulfonic acid (DNBS) resolves by 6 weeks, but can subsequently be reactivated by stress plus a sub-threshold dose of DNBS, but not by DNBS alone.Stress reduced colonic mucin and increased colon permeability.Susceptibility to reactivation by stress required CD4+ lymphocytes and could be adoptively transferred.We conclude that stress reactivates experimental colitis by facilitating entry of luminal contents that activate previously sensitized CD4 cells in the colon.on July 26,
Pulmonary arterial hypertension masquerading as severe refractory asthma
Authors: L. Achouh, D. Montani, G. Garcia, X. Jaïs, A. M. Hamid, O. Mercier, G. Simonneau, M. Humbert
Journal: European Respiratory Journal (2008)

Once the diagnosis of pulmonary arterial hypertension is established, wheezing and chronic cough are rarely described during the course of the disease. The present study reports on two nonsmoking patients with severe pulmonary arterial hypertension, confirmed by right-heart catheterisation, who developed chronic cough, wheezing and irreversible obstructive lung disease masquerading as adult-onset severe refractory asthma. In both cases, extrinsic proximal airway obstruction by dilated pulmonary arteries was demonstrated by fibreoptic bronchoscopy and computed tomography of the chest. The present observations add dilatation of the central pulmonary arteries with compression of the mainstem bronchi to the list of masqueraders of asthma in patients with pulmonary arterial hypertension.
Inhibition of antigen-specific T lymphocyte activation by structurally related Ir gene-controlled polymers. II. Competitive inhibition of I-E-restricted, antigen-specific T cell responses.
Authors: K L Rock, B Benacerraf
Journal: The Journal of Experimental Medicine (1984)

Our previous studies have defined a highly specific competitive inhibition between a pair of structurally related antigens (GT and GAT) for antigen presentation by accessory cells. The present report investigates this phenomenon in a second antigenic system, which is controlled by a distinct Ir gene product. Two GL phi-specific, I-Ed-restricted, interleukin 2-producing T cell hybridomas were constructed. The antigenic fine specificity of these two hybrid clones was distinct. One hybrid reacted solely with GL phi while the second cross-reacted with GLleu and GLT. These latter two copolymers, as well as the antigen GL, were found to inhibit the GL phi response of the non-cross-reactive hybrid. The structurally related antigen G phi was not inhibitory for this clone's response. The cross-reactive GL phi hybrid could also be inhibited, but, in this case, G phi and not GL caused the inhibition. Reciprocal inhibitions could be demonstrated between these and other hybrids (e.g., GAT responsive), indicating a very high degree of specificity to the inhibition. The inhibition caused by the various copolymers was reversible by increasing the concentration of GL phi, This effect was localized to the antigen-presenting cell and not the T cell hybridoma. Functionally, this competition did not appear to be for antigen uptake or general antigen processing. These findings generalize the phenomenon of antigen competition to a second antigen system in the context of a second Ia molecule. The possible mechanisms accounting for the complex pattern of specificities in this system are discussed.
The importance of folate, zinc and antioxidants in the pathogenesis and prevention of subfertility
Authors: I.M.W. Ebisch, C.M.G. Thomas, W.H.M. Peters, D.D.M. Braat, R.P.M. Steegers-Theunissen
Journal: Human Reproduction Update (2006)

Current treatments of subfertile couples are usually empiric, as the true cause of subfertility often remains unknown. Therefore, we outline the role of nutritional and biochemical factors in reproduction and subfertility. A literature search was performed using MEDLINE, Science Direct and bibliographies of published work with both positive and negative results. The studies showed that folate has a role in spermatogenesis. In female reproduction, folate is also important for oocyte quality and maturation, implantation, placentation, fetal growth and organ development. Zinc has also been implicated in testicular development, sperm maturation and testosterone synthesis. In females, zinc plays a role in sexual development, ovulation and the menstrual cycle. Both folate and zinc have antioxidant properties that counteract reactive oxygen species (ROS). Thiols, such as glutathione, balance the levels of ROS produced by spermatozoa and influence DNA compaction and the stability and motility of spermatozoa. Oocyte maturation, ovulation, luteolysis and follicle atresia are also affected by ROS. After fertilization, glutathione is important for sperm nucleus decondensation and pronucleus formation. Folate, zinc, ROS and thiols affect apoptosis, which is important for sperm release, regulation of follicle atresia, degeneration of the corpus luteum and endometrial shedding. Therefore, the concentrations of these nutrients may have substantial effects on reproduction. In conclusion, nutritional and biochemical factors affect biological processes in male and female reproduction. Further research should identify pathways that may lead to improvements in care and treatment of subfertility.
Cutaneous findings in sporadic and familial autosomal dominant hyper-IgE syndrome: A retrospective, single-center study of 21 patients diagnosed using molecular analysis
Authors: Amani Olaiwan, Marie-Olivia Chandesris, Sylvie Fraitag, Olivier Lortholary, Olivier Hermine, Alain Fischer, Yves de Prost, Capucine Picard, Christine Bodemer
Journal: Journal of the American Academy of Dermatology (2011)