Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Novel Broad-Range Real-Time PCR Assay for Rapid Detection of Human Pathogenic Fungi in Various Clinical Specimens

ABSTRACT In the present study, a novel broad-range real-time PCR was developed for the rapid detection of human pathogenic fungi. The assay targets a part of the 28S large-subunit ribosomal RNA (rDNA) gene. We investigated its application for the most important human pathogenic fungal genera, including Aspergillus, Candida, Cryptococcus, Mucor, Penicillium, Pichia, Microsporum, Trichophyton, and Scopulariopsis. Species were identified in PCR-positive reactions by direct DNA sequencing. A noncompetitive internal control was applied to prevent false-negative results due to PCR inhibition. The minimum detection limit for the PCR was determined to be one 28S rDNA copy per PCR, and the 95% detection limit was calculated to 15 copies per PCR. To assess the clinical applicability of the PCR method, intensive-care patients with artificial respiration and patients with infective endocarditis were investigated. For this purpose, 76 tracheal secretion samples and 70 heart valve tissues were analyzed in parallel by real-time PCR and cultivation. No discrepancies in results were observed between PCR analysis and cultivation methods. Furthermore, the application of the PCR method was investigated for other clinical specimens, including cervical swabs, nail and horny skin scrapings, and serum, blood, and urine samples. The combination of a broad-range real-time PCR and direct sequencing facilitates rapid screening for fungal infection in various clinical specimens.
Effect of maternal behavior on regulation during feeding in healthy infants and infants with transposition.

OBJECTIVE To compare physiological regulation and the effect of maternal sensitive caregiving during feeding on physiological regulation in healthy infants and in infants with transposition of the great arteries. DESIGN Descriptive, 2 groups, repeated measures. SETTING Three children's hospitals in the Midwest. PARTICIPANTS A convenience sample of 15 infants with transposition of the great arteries matched with 16 healthy infants. METHODS Measures of physiological regulation before, during, and after feeding and quality of maternal affect and behavior during feeding were collected postoperatively at 2 weeks and 2 months of age. RESULTS At 2 weeks, infants with transposition of the great arteries demonstrated impaired physiological regulation with feedings when compared with healthy infants. Healthy infants of more sensitive mothers were more likely to demonstrate a physiologically adaptive response during feeding. Maternal effect on physiological regulation was not observed in infants with transposition of the great arteries. No differences between groups were found at 2 months. CONCLUSIONS For infants with transposition of the great arteries, effects of surgical recovery and limited contact with their mothers relative to healthy infants may have outweighed the supportive effect of maternal sensitivity during feeding in the early weeks of life. Further research is needed to identify ways of enhancing the regulatory effect of maternal behavior on infants with heart defects.
Screening for biomarkers of spermatogonia within the human testis: a whole genome approach.

BACKGROUND A key step in studying the biology of spermatogonia is to determine their global gene expression profile. However, disassociation of these cells from the testis may alter their profile to a considerable degree. To characterize the molecular phenotype of human spermatogonia, including spermatogonial stem cells (SSCs), within their cognate microenvironment, a rare subtype of human defective spermatogenesis was exploited in which spermatogonia were the only germ cell type. METHODS The global expression profile of these samples was assessed on the Affymetrix microarray platform and compared with tissues showing homogeneous Sertoli-cell-only appearance; selected genes were validated by quantitative real-time PCR and immunohistochemistry on disparate sample sets. RESULTS Highly significant differences in gene expression levels correlated with the appearance of spermatogonia, including 239 best candidates of human spermatogonially expressed genes. Specifically, fibroblast growth factor receptor 3 (FGFR3), desmoglein 2 (DSG2), E3 ubiquitin ligase c-CBL (casitas B-cell lymphoma), cancer/testis antigen NY-ESO-1 (CTAG1A/B), undifferentiated embryonic cell transcription factor 1 (UTF1) and synaptosomal-associated protein, 91 kDa homolog (SNAP91) were shown to represent specific biomarkers of human spermatogonia. CONCLUSIONS These biomarkers, specifically the surface markers FGFR3 and DSG2, may facilitate the isolation and enrichment of human stem and/or progenitor spermatogonia and thus lay a foundation for studies of long-term maintenance of human SSCs/progenitor cells, spermatogonial self-renewal, clonal expansion and differentiation.
Dendrites, deep learning, and sequences in the hippocampus

The hippocampus places us both in time and space. It does so over remarkably large spans: milliseconds to years, and centimeters to kilometers. This works for sensory representations, for memory, and for behavioral context. How does it fit in such wide ranges of time and space scales, and keep order among the many dimensions of stimulus context? A key organizing principle for a wide sweep of scales and stimulus dimensions is that of order in time, or sequences. Sequences of neuronal activity are ubiquitous in sensory processing, in motor control, in planning actions, and in memory. Against this strong evidence for the phenomenon, there are currently more models than definite experiments about how the brain generates ordered activity. The flip side of sequence generation is discrimination. Discrimination of sequences has been extensively studied at the behavioral, systems, and modeling level, but again physiological mechanisms are fewer. It is against this backdrop that I discuss two recent developments in neural sequence computation, that at face value share little beyond the label “neural. ” These are dendritic sequence discrimination, and deep learning. One derives from channel physiology and molecular signaling, the other from applied neural network theory ‐ apparently extreme ends of the spectrum of neural circuit detail. I suggest that each of these topics has deep lessons about the possible mechanisms, scales, and capabilities of hippocampal sequence computation.
Causes and predictors of mortality in biopsy-proven lupus nephritis: the Sarawak experience

Abstract Background Lupus nephritis (LN) is a serious manifestation of systemic lupus erythematosus that can be fatal if left untreated. The causes and prognostic predictors of mortality in LN have been well studied in developed countries but evidence is lacking for developing countries. The objective of this study was to investigate the causes and predictors of mortality in a cohort of Malaysian patients with biopsy-proven LN. Methods We retrospectively studied all patients with biopsy-proven LN treated in Sarawak General Hospital during the period of 2000–15. Demographic data, clinical features and outcomes were collected. Cox regression analysis was carried out to determine the independent predictors of mortality. Results There was a total of 250 patients with 259 renal biopsies available for our analysis. Our patients were of multi-ethnic origins with a female predominance (90%). Their mean ± standard deviation age was 37.7 ± 12.8 years. The patients had a mean disease duration of 135.6 ± 81.9 months. Nephrotic syndrome was the most common presentation (29.6%) and acute renal failure was evident at initial presentation in 16% of patients. Class IV LN was the predominant biopsy class within the cohort (66.8%). The majority of patients achieved remission (81.2%) and had normal renal function (83.9%) at the last follow-up. The 5-, 10-, 15- and 20-year survival rates for our cohort were 93%, 88%, 82% and 77%, respectively. There were 37 deaths (14.8%), of which the main causes were: infection and flare (52.7%), infection alone (25.0%) and other causes (22.3%). Independent predictors of mortality in our cohort of LN patients were: the presence of acute kidney injury at presentation [hazard ratio (HR) 3.41; confidence interval (CI) 1.50–7.76], failure to achieve remission at 1-year post-induction therapy (HR 2.99; CI 1.35–6.65) and non-compliance with treatment (HR 1.89; CI 1.22–2.96). Age, ethnicity, class of LN and type of immunosuppressant used were not predictive of mortality. Conclusions Survival and renal outcomes in our LN cohort were comparable to most LN studies reported worldwide. Both flare and infection remained the main causes of death. The presence of acute renal failure at presentation, failure to achieve remission at 1 year post-treatment and non-compliance with treatment were independent prognostic predictors of mortality in LN.
Dopamine transporter proline mutations influence dopamine uptake, cocaine analog recognition, and expression

Analyses of mutation effects can aid in understanding how large proteins act. The dopamine transporter (DAT) mediates complex actions in recognizing cocaine and in recognizing and translocating dopamine, sodium, and chloride. DAT proline residues, especially those in transmembrane (TM) domains, are good candidates for involvement in these DAT actions. We now report production of mutants substituting alanine and/or glycine residues for 16 prolines located in or near putative DAT TM domains. We examine effects of these modifications on DAT expression, dopamine uptake, and cocaine analog binding. Mutants in prolines located in five DAT TM domains and four connecting loops alter apparent DAT membrane targeting. Five mutations decrease dopamine affinities more than threefold without significantly decreasing cocaine analog affinities. One decreases cocaine analog affinity without decreasing dopamine affinity. Two mutations decrease affinities for both dopamine and cocaine analog. P101 is especially implicated in dopamine uptake. Alanine substitution for this proline yields dopamine Vmax values of less than 3% of wild‐type values despite dopamine affinities more than fourfold higher than wild‐type and normal Na+ and Cl~ dependence. These DAT proline mutants identify DAT regions likely for dopamine translocation and for recognition of dopamine and cocaine. —Lin, Z. , Itokawa, M. , Uhl, G. R. Dopamine transporter proline mutations influence dopamine uptake, cocaine analog recognition, and expression. FASEB J. 14, 715–728 (2000)
Choice Behavior, Asset Integration and Natural Reference Points

Reference points play a major role in differentiating theories of choice under uncertainty. Under expected utility theory the reference point is implicit in the assumptions made about asset integration, which is the same thing as assuming different arguments of the utility function. Under prospect theory the reference point differentiates gains and losses, and the manner in which prospects are evaluated. We consider the implications for both models of allowing subjects to have natural reference points, in the sense that they derive from "homegrown" expectations about earnings in a dynamic task, rather than from a frame presumed by the observer. We elicit initial beliefs about expected earnings, and implement a dynamic decision process in which subjects could win or lose money, and even go bankrupt. In short, we cultivate a fertile and natural breeding ground for the effects of reference points to emerge. To characterize the latent data-generating process in a flexible statistical manner we assume that some observations are generated by an expected utility model and that some observations are generated by a cumulative prospect theory model. This specification leads to a finite mixture model in which reference points may be different from the frame presented by the lottery prizes. We report several striking findings. First, expected utility theory accounts for a large fraction of the observations, despite this setting providing a seemingly more natural breeding ground for prospect theory. Assuming homogenous, representative agents for each model type, expected utility theory accounts for b of the observations. With demographic heterogeneity controlled for it still accounts for ½ of the observations. Second, the expected utility theory subjects appear to have utility functions defined over their cumulative income over the sequence of tasks, rather than as defined over the prizes in each individual lottery choice. Finally, we identify demographic characteristics which differentiate the probability that a decision-maker used expected utility theory. Men are much more likely to use expected utility theory than women, racial minorities are more likely than others, those with higher grades are more likely, and those from poorer households are more likely. Thus our results provide insights into the domain of applicability of each of the major choice models, rather than claiming one to be the sole, true model.
Assessing impact of regulatory risk on shareholders’ wealth

ABSTRACT Research indicates that regulatory risk increases required return on investment by investors and causes underinvestment in industries with high sunk costs. The effects of regulatory changes may be measured by estimating the abnormal returns associated with the event. The results may suggest to regulators what should be encouraged or avoided. This article utilizes a fixed effects regression to examine abnormal returns from changes in Philippine nationalization regulations. The results are consistent with extant literature. Supreme Court decisions, which increased uncertainty and regulatory risk, produced negative abnormal returns. The initial release of draft implementing rules did not produce statistically significant effects, but a succeeding draft favouring liberalization, produced positive abnormal returns.
Optimal Financial Aid Policies for Students

We study the optimal design of financial aid policies for college students. The total social benefits of college education exceed the private benefits because the government receives a share of the monetary returns in the form of income taxes. We underscore the policy implications of this fiscal externality in an optimal dynamic public finance framework. The model incorporates multidimensional heterogeneity, idiosyncratic risk and borrowing constraints. It matches key empirical results on college enrollment patterns, returns to education and enrollment elasticities. We find that a marginal increase in college subsidies in the US is at least 70 percent self-financing through the net-present value increase in future tax revenue. When targeting this increase to children in the lowest parental income tercile, it is more than self-financing with a fiscal return of 165 percent. The optimal Mirrleesian income tax schedule is barely affected, in particular if subsidies are set at their optimal level.
Characterization of the Micro-Environment of the Testis that Shapes the Phenotype and Function of Testicular Macrophages

Macrophages are important in the activation of innate immune responses and in a tissue-specific manner in the maintenance of organ homeostasis. Testicular macrophages (TM), which reside in the testicular interstitial space, comprise the largest leukocyte population in the testes and are assumed to play a relevant function in maintaining testicular immune privilege. Numerous studies have indicated that the interstitial fluid (IF) surrounding the TM has immunosuppressive properties, which may influence the phenotype of TM. However, the identity of the immunosuppressive molecules present in the IF is poorly characterized. We show that the rat testicular IF shifted GM-CSF–induced M1 toward the M2 macrophage phenotype. IF-polarized M2 macrophages mimic the properties of TM, such as increased expression of CD163, high secretion of IL-10, and low secretion of TNF-α. In addition, IF-polarized macrophages display immunoregulatory functions by inducing expansion of immunosuppressive regulatory T cells. We further found that corticosterone was the principal immunosuppressive molecule present in the IF and that the glucocorticoid receptor is needed for induction of the testis-specific phenotype of TM. In addition, TM locally produce small amounts of corticosterone, which suppresses the basal expression of inflammatory genes as a means to render TM refractory to inflammatory stimuli. Taken together, these results suggest that the corticosterone present in the testicular environment shapes the immunosuppressive function and phenotype of TM and that this steroid may play an important role in the establishment and sustenance of the immune privilege of the testis.
Use of Extended Characteristics of Locomotion and Feeding Behavior for Automated Identification of Lame Dairy Cows

This study was carried out to detect differences in locomotion and feeding behavior in lame (group L; n = 41; gait score ≥ 2.5) and non-lame (group C; n = 12; gait score ≤ 2) multiparous Holstein cows in a cross-sectional study design. A model for automatic lameness detection was created, using data from accelerometers attached to the hind limbs and noseband sensors attached to the head. Each cow’s gait was videotaped and scored on a 5-point scale before and after a period of 3 consecutive days of behavioral data recording. The mean value of 3 independent experienced observers was taken as a definite gait score and considered to be the gold standard. For statistical analysis, data from the noseband sensor and one of two accelerometers per cow (randomly selected) of 2 out of 3 randomly selected days was used. For comparison between group L and group C, the T-test, the Aspin-Welch Test and the Wilcoxon Test were used. The sensitivity and specificity for lameness detection was determined with logistic regression and ROC-analysis. Group L compared to group C had significantly lower eating and ruminating time, fewer eating chews, ruminating chews and ruminating boluses, longer lying time and lying bout duration, lower standing time, fewer standing and walking bouts, fewer, slower and shorter strides and a lower walking speed. The model considering the number of standing bouts and walking speed was the best predictor of cows being lame with a sensitivity of 90.2% and specificity of 91.7%. Sensitivity and specificity of the lameness detection model were considered to be very high, even without the use of halter data. It was concluded that under the conditions of the study farm, accelerometer data were suitable for accurately distinguishing between lame and non-lame dairy cows, even in cases of slight lameness with a gait score of 2.5.
β‐Defensins chemoattract macrophages and mast cells but not lymphocytes and dendritic cells: CCR6 is not involved

β‐Defensins are natural peptide antibiotics whose immunomodulatory functions are poorly understood. In the present study, macrophages were found to migrate to human β‐defensins (HBD)‐1 to ‐4 using Gαi proteins as well as MAPK ERK, p38 and JNK as signal transducers. In addition, mast cells responded to HBD‐1 to ‐4 with calcium fluxes as well as chemotaxis, which increased upon stimulation with IgE plus antigen or ionomycin. In contrast, human β‐defensins were unable to induce migration of memory lymphocytes and dendritic cells (DC). Similar to HBD, the murine β‐defensin (mBD)‐8 mobilized macrophages and lacked the ability to recruit memory T cells. These findings were unexpected as CCR6 on memory T cells and DC has been previously observed to be a receptor for human β‐defensins. In support of our findings, however, RBL‐2H3 as well as 300.19 cells stably expressing CCR6 proved to be unresponsive to HBD‐2 and ‐3. Intriguingly, our observation of a PKC‐independent homologous desensitization between HBD‐1 to ‐4 suggests a common receptor for HBD. In summary, chemoattraction of macrophages and mast cells is evolutionary conserved within the β‐defensin family despite a considerable sequence variation and distinct antimicrobial activities. However, CCR6 is not a functional receptor for β‐defensins.
Delineation of Gliomas with Magnetic Resonance Imaging Using Gd-DTPA in Comparison with Computed Tomography and Positron Emission Tomography

Fourteen patients with cerebral gliomas were investigated by MR imaging using Gd-DTPA (Magnevist), CT with the contrast agent iohexol (Omnipaque) and, as a reference, positron emission tomography (PET) using 11C-L-methionine. Tumour areas with disruption of the blood-brain-barrier (BBB) as seen on MR and CT were compared with areas with increased accumulation of methionine in PET. There were 6 patients with high-grade astrocytoma (grade III-IV), 5 with low-grade astrocytoma (grade I–II) and 3 with oligodendroglioma. In 4 high-grade tumours, PET showed a larger tumour or tumour tissue in additional areas, compared with enhancement on MR and CT, while in 2 cases the tumour extension was similar in the three modalities. In the low grade tumour group, the findings on PET differed from those on post-contrast MR or CT in 7 cases. In 3 of these cases, no disruption of the BBB was seen either on MR or on CT. In 2 of our 14 patients CT showed larger enhancement extension than MR and in 2 cases MR was superior to CT in this respect. The enhancement intensity was higher on MR in 4 patients and on CT in 2 patients. No definite difference in the delineation of tumour tissue between the T1 weighted SE sequences used was found. The gradient echo sequences FLASH and FISP gave limited information that was less than that provided by the T1 weighted SE sequences. A greater increase in signal intensity in T1 weighted images was usually seen 5 min post-contrast in the high-grade tumours than in the low-grade ones.
Anthropogenic Influence on Heavy Metals' Content in Natural Flora

The content of heavy metals in phytomass of plants in natural habitats and habitats subject to various degrees of anthropogenic influence was estimated by a method of atomic-absorption spectrometry. Concentration of manganese in phytomass of plants in polluted habitats changes from 46.42 to 158.94 mg per Kg of dry matter. At semi-aquatic and water plants of polluted habitats concentration of manganese in green mass is on average 111.05…190.34 mg per Kg . Average concentration of copper for plants of polluted habitats is 3.47…5.96 mg per Kg for background – 3.27 mg per Kg. Plants of semi-aquatic habitats are not inclined to copper accumulation. All terrestrial and semi-aquatic plants in technogenic territories contained iron in insignificant amount. Statistically significant invert correlation between content of iron and such metals, as cadmium, manganese, lead, and magnesium is noted. The value of zinc concentration in plants of technogenic habitats varied from 21.12 to 44.01 mg per Kg of dry matter, slightly exceeding that at plants of background habitats (28.75 mg per Kg ). Zinc content in phytomass of water plants is twice lower than of terrestrial plants (17.05…19.51 mg per Kg ). Concentrations of nickel in plants of background and technogenic habitats are close - 1.93 and 1.69 mg per Kg of dry matter accordingly. Concentration of cadmium in plants from technogenic habitats exceeds maximum allowable concentration (MAC). On the average for plants of polluted habitats the lead content is 1.11…1.15 mg per Kg for background – 0.6 mg. Average concentration of chrome in phytomass changes almost 50 times - from 0.21 mg per Kg to 11.56 mg per Kg .