Miracle-dz/UniFAR-FTUs huggingface dataset:
Variance reduction trends on 'boosted' classifiers

Ensemble classification techniques such as bagging, (Breiman, 1996a), boosting (Freund & Schapire, 1997) and arcing algorithms (Breiman, 1997) have received much attention in recent literature. Such techniques have been shown to lead to reduced classification error on unseen cases. Even when the ensemble is trained well beyond zero training set error, the ensemble continues to exhibit improved classification error on unseen cases. Despite many studies and conjectures, the reasons behind this improved performance and understanding of the underlying probabilistic structures remain open and challenging problems. More recently, diagnostics such as edge and margin (Breiman, 1997; Freund & Schapire, 1997; Schapire et al., 1998) have been used to explain the improvements made when ensemble classifiers are built. This paper presents some interesting results from an empirical study performed on a set of representative datasets using the decision tree learner C4.5 (Quinlan, 1993). An exponential-like decay in the variance of the edge is observed as the number of boosting trials is increased. i.e. boosting appears to ‘homogenise’ the edge. Some initial theory is presented which indicates that a lack of correlation between the errors of individual classifiers is a key factor in this variance reduction.
Hypothermia protects human neurons

Background and Aims Hypothermia provides neuroprotection after cardiac arrest, hypoxic-ischemic encephalopathy, and in animal models of ischemic stroke. However, as drug development for stroke has been beset by translational failure, we sought additional evidence that hypothermia protects human neurons against ischemic injury. Methods Human embryonic stem cells were cultured and differentiated to provide a source of neurons expressing β III tubulin, microtubule-associated protein 2, and the Neuronal Nuclei antigen. Oxygen deprivation, oxygen-glucose deprivation, and H2O2-induced oxidative stress were used to induce relevant injury. Results Hypothermia to 33°C protected these human neurons against H2O2-induced oxidative stress reducing lactate dehydrogenase release and Terminal deoxynucleotidyl transferase dUTP nick end labeling-staining by 53% (P ≤ 0·0001; 95% confidence interval 34·8–71·04) and 42% (P ≤ 0·0001; 95% confidence interval 27·5–56·6), respectively, after 24 h in culture. Hypothermia provided similar protection against oxygen-glucose deprivation (42%, P ≤ 0·001, 95% confidence interval 18·3–71·3 and 26%, P ≤ 0·001; 95% confidence interval 12·4–52·2, respectively) but provided no protection against oxygen deprivation alone. Protection (21%) persisted against H2O2-induced oxidative stress even when hypothermia was initiated six-hours after onset of injury (P ≤ 0·05; 95% confidence interval 0·57–43·1). Conclusion We conclude that hypothermia protects stem cell-derived human neurons against insults relevant to stroke over a clinically relevant time frame. Protection against H2O2-induced injury and combined oxygen and glucose deprivation but not against oxygen deprivation alone suggests an interaction in which protection benefits from reduction in available glucose under some but not all circumstances.
How mini can minipterional craniotomies get?

To the Editor: In their recent article, Caplan et al revisit the minipterional approach to aneurysms of the anterior circulation as an acceptable alternative to the traditional pterional craniotomy standardized by Yasargil. This report is yet another illustration of the current effort in aneurysm microsurgery to adopt a minimally invasive stance. However, although intuitively plausible, it is not yet clear whether minicraniotomies truly do lead to better results; too small might in fact lead to worse outcomes, related to potential intraoperative difficulties due to an inadequate exposure and the need for greater tissue retraction. The authors point out that a new approach should not sacrifice surgical efficacy for shorter hospital stays (which might in fact be longer than usual if approach-related complications occur) or for the sake of cosmetics. In other words, a novel approach has to, at least, meet the same previously achieved results. This consideration implies that the identification of the core elements for aneurysm clipping is required, and that a surgical approach be strictly limited to these for it to be truly minimally invasive. We see these core elements as the following: the surgeon's experience; the aneurysm's angio-architecture and that of neighboring vessels; the
Bookly: An Interactive Everyday Artifact Showing the Time of Physically Accumulated Reading Activity

We introduce Bookly, an interactive artifact that physically represents the accumulated time of users' reading activity through abstract volumetric changes. Bookly accumulates the time of actions (e.g., picking up and putting down books) that users performed for reading and provides a designated space for the ongoing book being read. The results of our 2-week in-field study with six participants showed that continuous exposure to volumetric changes representing the accumulated time of reading activities helped the users to understand their unsettled reading patterns. Bookly also motivated the users to improve their reading behavior by gradually making reading part of their schedules. Additionally, the definite distinction of the ongoing book improved its visual affordance and accessibility for the users to start reading books. Based on the findings, we confirmed the possibility of making intangible data physical for self-reflection to enhance changes in behaviors that are difficult to perform due to weak motivation.
Human Influenza A Virus (H5N1) Detection by a Novel Multiplex PCR Typing Method

ABSTRACT We report the use of ResPlex III for genotyping influenza A viruses. The performance characteristics of the assay with regard to H5N1 are further evaluated. The ResPlex system incorporates a novel multiplex PCR technology, target-enriched multiplex PCR, to simultaneously amplify multiple molecular targets in one reaction. The ResPlex III assay targets the H1, H2, H3, H5, H7, H9, N1, and N2 genes from the influenza A virus as well as the NS genes from influenza A (NSA) and B (NSB) viruses, providing detection and genotyping of influenza A and B viruses. The analytical sensitivities for detecting the H5, N1, and NSA genes were 1, 10−1, and 10 50% tissue culture infectious doses/200 μl/reaction, respectively. A total of 217 sequential clinical samples including 14 samples with human H5N1 infections were tested by the ResPlex III assay, and the results were compared to a reference standard combined with results of viral culture and conventional reverse transcriptase and real-time PCR. The clinical sensitivity and specificity for detecting H5N1 were 93.3% and 100%, respectively, indicating that different subtypes of influenza A virus can be quickly and correctly identified using the ResPlex III genotyping approach.
Voluntary Explicit versus Involuntary Conceptual Memory Are Associated with Dissociable fMRI Responses in Hippocampus, Amygdala, and Parietal Cortex for Emotional and Neutral Word Pairs

Although functional neuroimaging studies have supported the distinction between explicit and implicit forms of memory, few have matched explicit and implicit tests closely, and most of these tested perceptual rather than conceptual implicit memory. We compared event-related fMRI responses during an intentional test, in which a group of participants used a cue word to recall its associate from a prior study phase, with those in an incidental test, in which a different group of participants used the same cue to produce the first associate that came to mind. Both semantic relative to phonemic processing at study, and emotional relative to neutral word pairs, increased target completions in the intentional test, but not in the incidental test, suggesting that behavioral performance in the incidental test was not contaminated by voluntary explicit retrieval. We isolated the neural correlates of successful retrieval by contrasting fMRI responses to studied versus unstudied cues for which the equivalent “target” associate was produced. By comparing the difference in this repetition-related contrast across the intentional and incidental tests, we could identify the correlates of voluntary explicit retrieval. This contrast revealed increased bilateral hippocampal responses in the intentional test, but decreased hippocampal responses in the incidental test. A similar pattern in the bilateral amygdale was further modulated by the emotionality of the word pairs, although surprisingly only in the incidental test. Parietal regions, however, showed increased repetition-related responses in both tests. These results suggest that the neural correlates of successful voluntary explicit memory differ in directionality, even if not in location, from the neural correlates of successful involuntary implicit (or explicit) memory, even when the incidental test taps conceptual processes.
Collaborating with People Like Me: Ethnic Co-Authorship within the Us

This study examines the ethnic identity of authors in over 2.5 million scientific papers written by US-based authors from 1985 to 2008, a period in which the frequency of English and European names among authors fell relative to the frequency of names from China and other developing countries. We find that persons of similar ethnicity co-author together more frequently than predicted by their proportion among authors. Using a measure of homophily for individual papers, we find that greater homophily is associated with publication in lower impact journals and with fewer citations, even holding fixed the authors' previous publishing performance. By contrast, papers with authors in more locations and with longer reference lists get published in higher impact journals and receive more citations than others. These findings suggest that diversity in inputs by author ethnicity, location, and references leads to greater contributions to science as measured by impact factors and citations.
20(S)-Protopanaxadiol Inhibition of Progression and Growth of Castration-Resistant Prostate Cancer

Castration-resistant progression of prostate cancer after androgen deprivation therapies remains the most critical challenge in the clinical management of prostate cancer. Resurgent androgen receptor (AR) activity is an established driver of castration-resistant progression, and upregulation of the full-length AR (AR-FL) and constitutively-active AR splice variants (AR-Vs) has been implicated to contribute to the resurgent AR activity. We reported previously that ginsenoside 20(S)-protopanaxadiol-aglycone (PPD) can reduce the abundance of both AR-FL and AR-Vs. In the present study, we further showed that the effect of PPD on AR expression and target genes was independent of androgen. PPD treatment resulted in a suppression of ligand-independent AR transactivation. Moreover, PPD delayed castration-resistant regrowth of LNCaP xenograft tumors after androgen deprivation and inhibited the growth of castration-resistant 22Rv1 xenograft tumors with endogenous expression of AR-FL and AR-Vs. This was accompanied by a decline in serum prostate-specific antigen levels as well as a decrease in AR levels and mitoses in the tumors. Notably, the 22Rv1 xenograft tumors were resistant to growth inhibition by the next-generation anti-androgen enzalutamide. The present study represents the first to show the preclinical efficacy of PPD in inhibiting castration-resistant progression and growth of prostate cancer. The findings provide a rationale for further developing PPD or its analogues for prostate cancer therapy.
Comparison of Methods for Detection of Vaccinia Virus in Patient Specimens

ABSTRACT We analyzed a shell vial culture assay (SVA), real-time PCR, and a direct fluorescent antibody assay (DFA) for rapid detection of vaccinia virus from vaccination sites of Dryvax vaccine recipients. Of 47 samples assayed, 100% were positive by PCR, 89% were positive by SVA, and 40% were positive by DFA. DFA was limited by the need for adequate numbers of cells, with 32% of samples inadequate for interpretation. DFA performed better with specimens from patients who had not previously received the vaccine. PCR was positive for longer times postvaccination than was SVA. Infectious virus could be recovered after 45 min of acetone fixation of shell vial coverslips. Commercially available polyclonal antibodies cross-reacted with other orthopoxviruses and herpes simplex 1, but commercially available monoclonal antibodies were specific for vaccinia virus. In summary, PCR was the most sensitive test for detecting vaccinia virus in clinical specimens, while the DFA was the most rapid but the least sensitive test.
Mechanisms of folate homeostasis.

Recent work has provided information that allows the delineation of the mechanisms by which folate homeostasis is maintained. Dietary folates are converted to monoglutamates in the gut, absorbed by an active process, and distributed to tissues by the enterohepatic cycle, possibly utilizing folic acid binding proteins. During short periods of dietary deprivation, supply is maintained in the monoglutamate pools in the enterohepatic cycle as well as within cells. A net increase in available folate results from a decrease in tissue uptake and in subsequent polyglutamate synthesis, coupled with a fixed rate of conversion of polyglutamate to monoglutamate and release from the cell. The liver exerts substantial regulatory effect because of its mass, relatively rapid folate turnover, and the large folate flux through the enterohepatic cycle. In addition, there is a substantial, if more long-term, contribution from tissues that die and release folates (e.g., red blood cells), and a pathway exists that is capable of salvaging this folate and returning it to the liver for subsequent redistribution to actively proliferating cells.
Depressive symptoms, self-esteem, HIV symptom management self-efficacy and self-compassion in people living with HIV

The aims of this study were to examine differences in self-schemas between persons living with HIV/AIDS with and without depressive symptoms, and the degree to which these self-schemas predict depressive symptoms in this population. Self-schemas are beliefs about oneself and include self-esteem, HIV symptom management self-efficacy, and self-compassion. Beck's cognitive theory of depression guided the analysis of data from a sample of 1766 PLHIV from the USA and Puerto Rico. Sixty-five percent of the sample reported depressive symptoms. These symptoms were significantly (p ≤ 0.05), negatively correlated with age (r = −0.154), education (r = −0.106), work status (r = −0.132), income adequacy (r = −0.204, self-esteem (r = −0.617), HIV symptom self-efficacy (r = − 0.408), and self-kindness (r = − 0.284); they were significantly, positively correlated with gender (female/transgender) (r = 0.061), white or Hispanic race/ethnicity (r = 0.047) and self-judgment (r = 0.600). Fifty-one percent of the variance (F = 177.530 (df = 1524); p < 0.001) in depressive symptoms was predicted by the combination of age, education, work status, income adequacy, self-esteem, HIV symptom self-efficacy, and self-judgment. The strongest predictor of depressive symptoms was self-judgment. Results lend support to Beck's theory that those with negative self-schemas are more vulnerable to depression and suggest that clinicians should evaluate PLHIV for negative self-schemas. Tailored interventions for the treatment of depressive symptoms in PLHIV should be tested and future studies should evaluate whether alterations in negative self-schemas are the mechanism of action of these interventions and establish causality in the treatment of depressive symptoms in PLHIV.
Expression of vanilloid receptor TRPV1 in the rat trigeminal sensory nuclei

Little is known about the central projection patterns of trigeminal afferent neurons expressing the vanilloid receptor TRPV1 and their coexpression of neuromodulatory peptides. To address these issues, we examined the distribution of TRPV1‐positive neurons in the trigeminal ganglion (TG) and trigeminal sensory nuclei principalis (Vp), oralis (Vo), interpolaris (Vi), and caudalis (Vc) in the rat via light and electron microscopy. In addition, we studied the colocalization of TRPV1‐positive neurons with substance P (SP) and calcitonin gene‐related peptide (CGRP) via confocal microscopy. In TG, only small and medium‐sized neurons were immunopositive for TRPV1. The staining for TRPV1 was found in axon collaterals in the dorsal parts of Vp, Vo, and Vi and in terminals and fibers throughout lamina I and the outer zone of lamina II (IIo) of Vc. With electron microscopy, TRPV1‐positive fibers in the ascending and descending trigeminal tracts were found to be unmyelinated. Almost all TRPV1‐positive terminals in Vc contained numerous large dense‐core vesicles and formed synaptic contacts with single small dendrites. Multiple immunofluorescence revealed a high degree of colocalization of TRPV1 with SP and CGRP in TG neurons as well as in fibers and terminals confined to laminae I and IIo of Vc. These results suggest that the central projections of unmyelinated (C) afferents sensitive to noxious heat and capsaicin are organized differently between Vc and the rostral trigeminal nuclei and that Vc may play a role in the development of hyperalgesia. J. Comp. Neurol. 478:62–71, 2004. © 2004 Wiley‐Liss, Inc.
Ongoing global biodiversity loss and the need to move beyond protected areas: a review of the technical and practical shortcomings of protected areas on land and sea

A leading strategy in international efforts to reverse ongoing losses in biodiversity is the use of protected areas. We use a broad range of data and a review of the literature to show that the effectiveness of existing, and the current pace of the establishment of new, protected areas will not be able to overcome current trends of loss of marine and terrestrial biodiversity. Despite local suc- cesses of well-designed and well-managed protected areas proving effective in stemming biodiver- sity loss, there are significant shortcomings in the usual process of implementation of protected areas that preclude relying on them as a global solution to this problem. The shortcomings include techni- cal problems associated with large gaps in the coverage of critical ecological processes related to individual home ranges and propagule dispersal, and the overall failure of such areas to protect against the broad range of threats affecting ecosystems. Practical issues include budget constraints, conflicts with human development, and a growing human population that will increase not only the extent of anthropogenic stressors but the difficulty in successfully enforcing protected areas. While efforts towards improving and increasing the number and/or size of protected areas must continue, there is a clear and urgent need for the development of additional solutions for biodiversity loss, par- ticularly ones that stabilize the size of the world's human population and our ecological demands on biodiversity.
Assessment of Breast Cancer Risk in an Iranian Female Population Using Bayesian Networks with Varying Node Number

Objective: As a source of information, medical data can feature hidden relationships. However, the high volume of datasets and complexity of decision-making in medicine introduce difficulties for analysis and interpretation and processing steps may be needed before the data can be used by clinicians in their work. This study focused on the use of Bayesian models with different numbers of nodes to aid clinicians in breast cancer risk estimation. Methods: Bayesian networks (BNs) with a retrospectively collected dataset including mammographic details, risk factor exposure, and clinical findings was assessed for prediction of the probability of breast cancer in individual patients. Area under the receiver-operating characteristic curve (AUC), accuracy, sensitivity, specificity, and positive and negative predictive values were used to evaluate discriminative performance. Result: A network incorporating selected features performed better (AUC = 0.94) than that incorporating all the features (AUC = 0.93). The results revealed no significant difference among 3 models regarding performance indices at the 5% significance level. Conclusion: BNs could effectively discriminate malignant from benign abnormalities and accurately predict the risk of breast cancer in individuals. Moreover, the overall performance of the 9-node BN was better, and due to the lower number of nodes it might be more readily be applied in clinical settings.
Eye movements during listening reveal spontaneous grammatical processing

Recent research using eye-tracking typically relies on constrained visual contexts in particular goal-oriented contexts, viewing a small array of objects on a computer screen and performing some overt decision or identification. Eyetracking paradigms that use pictures as a measure of word or sentence comprehension are sometimes touted as ecologically invalid because pictures and explicit tasks are not always present during language comprehension. This study compared the comprehension of sentences with two different grammatical forms: the past progressive (e.g., was walking), which emphasizes the ongoing nature of actions, and the simple past (e.g., walked), which emphasizes the end-state of an action. The results showed that the distribution and timing of eye movements mirrors the underlying conceptual structure of this linguistic difference in the absence of any visual stimuli or task constraint: Fixations were shorter and saccades were more dispersed across the screen, as if thinking about more dynamic events when listening to the past progressive stories. Thus, eye movement data suggest that visual inputs or an explicit task are unnecessary to solicit analog representations of features such as movement, that could be a key perceptual component to grammatical comprehension.
Variability in the Rate of Cold Acclimation and Deacclimation among Tuber-bearing Solanum (Potato) Species

ADDITIONAL INDEX WORDS. Solanum species, cold acclimation, cold deacclimation ABSTRACT. Two major components of frost resistance are freezing tolerance in the nonacclimated state (growing in normal condition) and capacity to cold acclimate (increase in freezing tolerance upon exposure to chilling temperatures). In addition to these two major components, numerous factors contribute to frost survival. Although the rate of cold acclimation and deacclimation have been recognized as important factors contributing to frost survival, very little information about them is available. Our objective was to determine if there is variability in the rate of cold acclimation and deacclimation among tuber-bearing wild potato species: S. acaule Bitter, S. commersonii Dunal, S. megistacrolobum Bitter, S. multidissectum Hawkes, S. polytrichon Rydb. , S. sanctae-rosae Hawkes, and S. megistacrolobum subsp. toralapanum (Cardenas & Hawkes) GiannattasioS (ii) late acclimators; (iii) progressive acclimators, and (iv) nonacclimators. Likewise, a wide range of cold deacclimation behavior was found. Some species showed as low a loss of 20% of their freezing tolerance, others showed as much as >60% loss after 12 hours of deacclimation. Significant deacclimation was observed in all cold acclimating species after 1 day. These results demonstrate that the rates of cold acclimation and deacclimation were not necessarily related to the cold acclimation capacity of a species. Rapid acclimation in response to low temperatures preceding a frost episode and slow deacclimation in response to unseasonably warm daytime temperatures could be advantageous for plants to survive frost events. Thus, in addition to nonacclimated freezing tolerance and acclimation capacity, it would be very desirable to be able to select for rapid acclimation and slow deacclimation abilities. Results demonstrate that variability for these two traits exists in Solanum L. (potato) species.