Miracle-dz/UniFAR-FTUs huggingface dataset:
Parkinson's disease – the continuing search for biomarkers

Abstract There is currently no well-established biomarker for Parkinson's disease. The need to better diagnose the condition, define the subtypes of disease, and follow its course independent of any symptomatic drug effects is well-established. In this review, we will begin by reviewing the evidence for biological fluid biomarkers in Parkinson's disease. We will then touch upon the role of brain imaging in diagnosis and defining prognosis, as well as the value of studying motor phenotype and its potential applications for characterising Parkinson's disease subtypes with differing natural histories.
Capecitabine, Oxaliplatin and Radiotherapy: A Phase IB Neoadjuvant Study for Esophageal Cancer with Gene Expression Analysis

Purpose: To determine the maximal tolerated dose of capecitabine with oxaliplatin + radiotherapy in a phase I study of localized esophageal cancer. Patients and Methods: Oxaliplatin (85 mg/m2) administered on days 1, 15, and 29. Capecitabine administered twice daily 5 days weekly; dose levels (DL) were 1, 1000; 2, 1250; and 3, 1500 mg/m2 with 50.4 Gy radiation. Results: Dose-limiting toxicity was reached at DL 3. Carboxylesterase expression in day 2 tumor specimens and induction correlated with response (p ≤ 0.05). Conclusion: The maximal tolerated dose was 85 mg/m2 of oxaliplatin, 1,250 mg/m2/day of capecitabine, and 50.4 Gy of radiation.
Effects of pH and Sugar on Acetoin Production from Citrate by Leuconostoc lactis

The relationship between acetoin production and citrate utilization in Leuconostoc lactis NCW1 was studied. In a complex medium the organism utilized citrate at neutral pH (initial pH, 6.3) and at acid pH (initial pH, 4.5) but produced nine times more acetoin at the latter pH. In resting cells the utilization of citrate was optimum at pH 5.3. Production of acetoin as a function of citrate utilization increased as the pH decreased, and at pH 4.3 all of the citrate utilized was recovered as acetoin. Glucose (10 mM) and lactose (10 mM) markedly stimulated citrate utilization but totally inhibited acetoin production in glucose- and lactose-grown cells. Addition of glucose to cells actively metabolizing citrate caused an immediate increase in citrate uptake and a reduction in the level of acetoin. The apparent Km values of lactic dehydrogenase for pyruvate were 1.05, 0.25, and 0.15 mM at pH 7.5, 6.5, and 5.0, respectively. Several heterofermentation intermediates inhibited α-acetolactate synthetase and decarboxylase activities. The implications of these results in regulating acetoin formatin are discussed.
(Sub)millimetre interferometric imaging of a sample of COSMOS/AzTEC submillimetre galaxies III. Environments

We study the environment of 23 submillimetre galaxies (SMGs) drawn from the JCMT/AzTEC 1.1mm S/N-limited sample in the COSMOS field, as well as 4 COSMOS SMGs at z_spec>4.5, and 1 at z_spec=2.49, yielding a sample of 28 SMGs. We search for overdensities using the COSMOS photometric redshifts based on over 30 UV-NIR photometric bands, reaching an accuracy of sigma(Delta z/(1+z))=0.0067 (0.0155) at z 3.5). To identify overdensities we apply the Voronoi tessellation analysis, and estimate the overdensity estimator delta_g as a function of distance from the SMG and/or overdensity center. We test and validate our approach via simulations, X-ray detected groups, and spectroscopic verifications using VUDS and zCOSMOS catalogues showing that even with photometric redshifts in COSMOS we can efficiently retrieve overdensities out to z~5. Our results yield that 11/23 (48%) JCMT/AzTEC 1.1mm SMGs occupy overdense environments. Considering the entire JCMT/AzTEC 1.1mm S/N>4 sample, and accounting for the expected fraction of spurious detections, yields that 35-61% of the SMGs in the S/N-limited sample occupy overdense environments. We perform an X-ray stacking analysis in the 0.5-2keV band using a 32" aperture and our SMG positions, and find statistically significant detections. For our z 2] subsample we find an average flux of (4.0+/-0.8)x10^{-16} [(1.3+/-0.5)x10^{-16}] erg/s/cm^2 and a corresponding total mass of M_200 = 2.8x10^{13} [2x10^{13}] MSol. Our results suggest a higher occurrence of SMGs occupying overdense environments at z>3, than at z<3. This may be understood if highly star forming galaxies can only be formed in the highest peaks of the density field tracing the most massive dark matter haloes at early cosmic epochs, while at later times cosmic structure may have matured sufficiently that more modest overdensities correspond to sufficiently massive haloes to form SMGs.
Systemizing Colour for Conceptual Modeling

Colour is used in many conceptual models and is discussed intensively since M OODY has published his ‘Physics of Notation’. Yet, choosing the right colour for a construct is difficult but crucial. Using a colour for a certain construct which is not appropriate can lead to visual stress as well as too much or too little emphasis on that construct. The aim of this paper is to give a systematization of colour for conceptual modeling by reviewing theories of colour vision, colour harmony and visual attention. Based on this review we provide colour combinations for different conceptual modeling colour scenarios.
Effects of interleukin‐3 following chemotherapy of non‐Hodgkin's lymphoma. A prospective, controlled phase I/II study.

Abstract: The effect of rhIL‐3 was investigated in 32 patients with newly diagnosed non‐Hodgkin lymphoma in a phase I/II trial. All patients received 6 cycles of standard CHOP chemotherapy, and each patient was his own control where rhIL‐3 was given as a daily s.c. injection for 14 days (day 2–15) in cycle 2 and 4, while cycle 1 and 3 were control cycles. Five dose levels were examined (0.5 — 1 — 5 — 7.5 — 10 μg/kg). Compared to the other more lineage‐specific hemopoietic growth factors G‐ and GM‐CSF, the effect of rhIL‐3 on the hemopoiesis was less dramatic and more delayed, i.e. the most apparent effect was observed in the 2 weeks of treatment. Thus, the neutrophil counts from days 15 to 22 following CHOP were significantly raised and the duration of neutropenia was shorter (significantly only at 10 μg/kg), while the nadir values were unaffected. Platelet recovery from days 12–22 was significantly increased and nadir values occurred earlier compared to control cycles, but were only increased in some subsets. Other cell populations affected moderately in the recovery period were eosinophils and monocytes. Reticulocytes increased, but no effect on hemoglobin or RBC transfusion requirement was noted. Only moderate adverse reactions occurred such as fever, chills, flushing of the face and flu‐like symptoms. There was no evidence of stimulation of tumor growth. Most significant, the rhIL‐3 treatment at all but the lowest dose levels led to an improved tolerance to chemotherapy, as indicated by a decline in number of delayed cycles. A conclusion concerning the role of rhIL‐3 as post‐chemotherapy adjuvant should await studies using rhIL‐3 in combination with more lineage‐restricted hemopoietic growth factors.
Isolation of five rice nonendosperm tissue‐expressed promoters and evaluation of their activities in transgenic rice

Summary Using promoters expressed in nonendosperm tissues to activate target genes in specific plant tissues or organs with very limited expression in the endosperm is an attractive approach in crop transgenic engineering. In this article, five putative nonendosperm tissue‐expressed promoters were cloned from the rice genome and designated PO s NETE 1, PO s NETE 2, PO s NETE 3, PO s NETE 4 and PO s NETE 5. By qualitatively and quantitatively examining GUSplus reporter gene expression in transgenic rice plants, PO s NETE 1‐PO s NETE 5 were all found to be active in the roots, leaves, stems, sheaths and panicles but not in the endosperm of plants at different developmental stages. In addition, PO s NETE 2, PO s NETE 4 and PO s NETE 5 were also inactive in rice embryos. Among these promoters, PO s NETE 4 and PO s NETE 5 exhibited higher activities in all of the tested tissues, and their activities in stems, leaves, roots and sheaths were higher than or comparable to those of the rice Actin1 promoter. We also progressively monitored the activities of PO s NETE 1‐PO s NETE 5 in two generations of single‐copy lines and found that these promoters were stably expressed between generations. Transgenic rice was produced using PO s NETE 4 and PO s NETE 5 to drive a modified Bt gene, mC ry1Ab. Bt protein expressed in the tested plants ranged from 1769.4 to 4428.8 ng/g fresh leaves, whereas Bt protein was barely detected in the endosperm. Overall, our study identified five novel nonendosperm tissue‐expressed promoters that might be suitable for rice genetic engineering and might reduce potential social concern regarding the safety of GMO crops.
Identification of candidate molecular markers of nasopharyngeal carcinoma by microarray analysis of subtracted cDNA libraries constructed by suppression subtractive hybridization

To identify differentially expressed genes and scan candidate molecular markers in nasopharyngeal carcinoma (NPC). We constructed four subtracted cDNA libraries using suppression subtractive hybridization technique, then randomly picked about 1200 colonies from the libraries to construct cDNA microarray and analyzed the gene expression profile in 19 NPCs, three NPC-derived cell lines, and 10 chronic inflammation of nasopharyngeal mucosa tissue samples using the cDNA microarray. We used real-time quantitative reverse transcription polymerase chain reaction and in-situ hybridization techniques to confirm our microarray results. The results showed that there were 37 highly expressed colonies and 68 poorly expressed colonies in NPC. Thirty-two known genes were identified by sequencing 105 differentially expressed colonies in NPC. Palate, lung, and nasal epithelium carcinoma (PLUNC)-associated and homo sapien cell division cycle 37 homolog (Saccharomyces cerevisiae)-like 1 (CDC37L1) genes had a higher frequency than others in the 68 poorly expressed colonies in NPC. The frequency of signal transducer and activator of transcription 5A gene was the highest in the 37 highly expressed colonies in NPC; after that were member RAS oncogene family and secreted protein, acidic, cysteine-rich genes. Real-time quantitative reverse transcription-polymerase chain reaction and in-situ hybridization techniques confirmed that the NPC group had a lower frequency of PLUNC and CDC37L1 expression than the groups of chronic inflammation of nasopharyngeal mucosa (P<0.01). The data suggested that PLUNC and CDC37L1 genes might be the putative molecular markers of NPC. For the first time we found that there was a close relationship between CDC37L1 and NPC.
Understanding Overuse of Computed Tomography for Minor Head Injury in the Emergency Department: A Triangulated Qualitative Study.

BACKGROUND Overuse of computed tomography (CT) for minor head injury continues despite developed and rigorously validated clinical decision rules like the Canadian CT Head Rule (CCHR). Adherence to this sensitive and specific rule could decrease the number of CT scans performed in minor head injury by 35%. But in practice, the CCHR has failed to reduce testing, despite its accurate performance. OBJECTIVES The objective was to identify nonclinical, human factors that promote or inhibit the appropriate use of CT in patients presenting to the emergency department (ED) with minor head injury. METHODS This was a qualitative study in three phases, each with interview guides developed by a multidisciplinary team. Subjects were recruited from patients treated and released with minor head injuries and providers in an urban academic ED and a satellite community ED. Focus groups of patients (four groups, 22 subjects total) and providers (three groups, 22 subjects total) were conducted until thematic saturation was reached. The findings from the focus groups were triangulated with a cognitive task analysis, including direct observation in the ED (>150 hours), and individual semistructured interviews using the critical decision method with four senior physician subject matter experts. These experts are recognized by their peers for their skill in safely minimizing testing while maintaining patient safety and engagement. Focus groups and interviews were audio recorded and notes were taken by two independent note takers. Notes were entered into ATLAS.ti and analyzed using the constant comparative method of grounded theory, an iterative coding process to determine themes. Data were double-coded and examined for discrepancies to establish consensus. RESULTS Five core domains emerged from the analysis: establishing trust, anxiety (patient and provider), constraints related to ED practice, the influence of others, and patient expectations. Key themes within these domains included patient engagement, provider confidence and experience, ability to identify and manage patient anxiety, time constraints, concussion knowledge gap, influence of health care providers, and patient expectations to get a CT. CONCLUSIONS Despite high-quality evidence informing use of CT in minor head injury, multiple factors influence the decision to obtain CT in practice. Identifying and disseminating approaches and designing systems that help clinicians establish trust and manage uncertainty within the ED context could optimize CT use in minor head injury.
Geochemical arguments for an Earth-like Moon-forming impactor

Geochemical evidence suggests that the material accreted by the Earth did not change in nature during Earth's accretion, presumably because the inner protoplanetary disc had uniform isotopic composition similar to enstatite chondrites, aubrites and ungrouped achondrite NWA 5363/5400. Enstatite meteorites and the Earth were derived from the same nebular reservoir but diverged in their chemical evolutions, so no chondrite sample in meteorite collections is representative of the Earth's building blocks. The similarity in isotopic composition (Δ17O, ϵ50Ti and ϵ54Cr) between lunar and terrestrial rocks is explained by the fact that the Moon-forming impactor came from the same region of the disc as other Earth-forming embryos, and therefore was similar in isotopic composition to the Earth. The heavy δ30Si values of the silicate Earth and the Moon relative to known chondrites may be due to fractionation in the solar nebula/protoplanetary disc rather than partitioning of silicon in Earth's core. An inversion method is presented to calculate the Hf/W ratios and ϵ182W values of the proto-Earth and impactor mantles for a given Moon-forming impact scenario. The similarity in tungsten isotopic composition between lunar and terrestrial rocks is a coincidence that can be explained in a canonical giant impact scenario if an early formed embryo (two-stage model age of 10–20 Myr) collided with the proto-Earth formed over a more protracted accretion history (two-stage model age of 30–40 Myr).
DNA Methylation Is Linked to Deacetylation of Histone H3, but Not H4, on the Imprinted Genes Snrpnand U2af1-rs1

ABSTRACT The relationship between DNA methylation and histone acetylation at the imprinted mouse genes U2af1-rs1 and Snrpnis explored by chromatin immunoprecipitation (ChIP) and resolution of parental alleles using single-strand conformational polymorphisms. TheU2af1-rs1 gene lies within a differentially methylated region (DMR), while Snrpn has a 5′ DMR (DMR1) with sequences homologous to the imprinting control center of the Prader-Willi/Angelman region. For both DMR1 of Snrpn and the 5′ untranslated region (5′-UTR) and 3′-UTR ofU2af1-rs1, the methylated and nonexpressed maternal allele was underacetylated, relative to the paternal allele, at all H3 lysines tested (K14, K9, and K18). For H4, underacetylation of the maternal allele was exclusively (U2af1-rs1) or predominantly (Snrpn) at lysine 5. Essentially the same patterns of differential acetylation were found in embryonic stem (ES) cells, embryo fibroblasts, and adult liver from F1 mice and in ES cells from mice that were dipaternal or dimaternal for U2af1-rs1. In contrast, in a region within Snrpn that has biallelic methylation in the cells and tissues analyzed, the paternal (expressed) allele showed relatively increased acetylation of H4 but not of H3. The methyl-CpG-binding-domain (MBD) protein MeCP2 was found, by ChIP, to be associated exclusively with the maternal U2af1-rs1 allele. To ask whether DNA methylation is associated with histone deacetylation, we produced mice with transgene-induced methylation at the paternal allele of U2af1-rs1. In these mice, H3 was underacetylated across both the parental U2af1-rs1 alleles whereas H4 acetylation was unaltered. Collectively, these data are consistent with the hypothesis that CpG methylation leads to deacetylation of histone H3, but not H4, through a process that involves selective binding of MBD proteins.
Lowering Foreign Language Anxiety through Self-Regulated Learning Strategy Use

Foreign language classroom anxiety (FLCA) and self-regulated learning strategies (SRLSs) are two important factors that influence language learning process in negative and positive ways respectively. The aim of this study was to explore the relationship between FLCA and SRLSs. To this end, 100 university students majoring in TEFL were selected. For collecting data, Foreign Language Classroom Anxiety Scale (Horwitz, Horwitz, & Cope, 1986) and Motivated Strategies for Learning Questionnaire (Pintrich & De Groot, 1990) were used. To analyze the data, Kendall correlation was run. The results revealed that there is a negative relationship between FLCA (communication apprehension, test anxiety, & fear of negative evaluation) and SRLSs (cognitive strategy use & self-regulation).
Joint Custody: Historical, Legal, and Clinical Perspectives with Emphasis on the Situation in Canada

The search for ways to mitigate the effects of family breakdown on parents and children includes legislative and clinical efforts which to some extent influence each other. In the past year much public interest has been aroused in Canada, and particularly in Ontario, in the issue of legislative changes which would make joint custody the usual or “preferred” legal disposition of custody cases. This paper provides a discussion of the legislated preference, or “rebut-table presumption” of joint custody from a historical, legal and clinical point of view. Definition and elaboration of what joint custody is from the legal and practical perspectives is provided with an emphasis on Canadian laws and practice. The legal rights of the non-custodial parent are explained, and relevant case law is highlighted. The relationship between joint custody, support orders and relitigation rates are elaborated. Following this is a critical overview of the empirical research on joint custody as it relates to the adjustment of children and parent satisfaction is included. It is concluded that while there is little question that shared parenting can be beneficial to children, the enthusiasm of legislators for joint custody has not been supported by empirical data. It is necessary to examine under what circumstances and for which kinds of parents and children joint custody might be beneficial since it is unlikely that one solution will fit the needs of all families and all stages of family life.
Profiles of violent youth: substance use and other concurrent problems.

OBJECTIVES This study examined the prevalence of various violent behaviors among high school-age adolescents, the co-occurrence of teenage violence with other public health problems, and gender differences in violence. METHODS Longitudinal data for more than 4500 high school seniors and dropouts from California and Oregon were used to develop weighted estimates of the prevalence of violent behavior and its co-occurrence with other emotional and behavioral problems. RESULTS More than half the sample had engaged in violence during the last year, and one in four had committed predatory violence. Boys were more likely than girls to engage in most types of violence, but both were equally prone to violence within the family. Violent youth were more likely than their peers to have poor mental health, use drugs, drop out of school, and be delinquent. Violent boys were more likely than violent girls to commit nonviolent felonies and sell drugs, but less likely to have poor mental health or become a parent. Prevalence estimates for violence co-occurring with three or more other problems ranged from 4% to 21%. CONCLUSIONS Teenage violence typically coexists with additional emotional and behavioral problems. Programs must consider the broader public health context in which violence occurs.
Effect of a mental health "carve-out" program on the continuity of antipsychotic therapy.

BACKGROUND On July 1, 1996, as a cost-containment strategy, Tennessee's expanded Medicaid program, TennCare, rapidly shifted the provision of mental health services to a fully capitated, specialty "carve-out" program, TennCare Partners. We studied the effect of this transition on the continuity of antipsychotic therapy among patients with severe mental illness who had previously adhered to treatment. METHODS Study patients were 21 to 64 years of age, were enrolled throughout the study period, and had adhered to antipsychotic therapy during a 6-month base-line period that preceded the 12 months of study follow-up. The study population included 4507 patients whose follow-up began on the day the change was implemented (the post-transition cohort) and 3644 patients whose follow-up began one year earlier (the pretransition cohort). We compared the two cohorts in terms of the loss of continuity of antipsychotic therapy (missed treatment for more than 60 days during follow-up) and the mean number of days of antipsychotic therapy during follow-up. RESULTS As compared with the pretransition cohort, the post-transition cohort had increased odds of loss of continuity (a multivariate odds ratio of 1.18 [95 percent confidence interval, 1.07 to 1.30], P=0.001) and a shorter mean duration of antipsychotic therapy (a mean reduction of 4.2 days [95 percent confidence interval, 1.7 to 6.7], P=0.001) during follow-up. This difference was most pronounced among high-risk patients (those requiring the administration of extended-release [depot] injections of antipsychotic medications or who had been hospitalized for psychosis) at base line, for whom continuity was most important (odds ratio for loss of continuity, 1.79 [95 percent confidence interval, 1.45 to 2.22]; P<0.001; mean reduction in the number of days of antipsychotic therapy, 14.4 days [95 percent confidence interval, 9.4 to 19.4]; P<0.001). These patients had decreased use of antipsychotic drugs immediately after the transition; the lower level persisted throughout the 12 months of follow-up. CONCLUSIONS These findings underscore the need to ensure that shifts to widely used carve-out programs, which are designed primarily to contain costs, do not adversely affect clinical outcomes.
Evaluating Online Labor Markets for Experimental Research: Amazon.com's Mechanical Turk

We examine the trade-offs associated with using Amazon.com's Mechanical Turk (MTurk) interface for subject recruitment. We first describe MTurk and its promise as a vehicle for performing low-cost and easy-to-field experiments. We then assess the internal and external validity of experiments performed using MTurk, employing a framework that can be used to evaluate other subject pools. We first investigate the characteristics of samples drawn from the MTurk population. We show that respondents recruited in this manner are often more representative of the U.S. population than in-person convenience samples—the modal sample in published experimental political science—but less representative than subjects in Internet-based panels or national probability samples. Finally, we replicate important published experimental work using MTurk samples.