Miracle-dz/UniFAR-FTUs huggingface dataset:
Ja n 20 05 Recoverable One-dimensional Encoding of Protein Three-dimensional Structures

Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how th e native three-dimensional (3D) structure of a protein is encoded in the amino acid seque nce. However, it has not been clear whether a given set of 1D structures contain su fficient information for recovering the underlying 3D structure. Here we show tha t e 3D structure of a protein can be recovered from a set of three types of 1D str uctures, namely, secondary structure, contact number and residue-wise cont act order which is introduced here for the first time. Using simulated annealing m olecular dynamics simulations, the structures satisfying the given native 1D structural restraints were sought for 16 proteins of various structural classes and of s izes ranging from 56 to 146 residues. By selecting the structures best satisfyin g the restraints, all the proteins showed the coordinate RMS deviation of less than 4 Å from the native structure, and for most of them, the deviation was even less t han 2̊A. The present result opens a new possibility to protein structure predict ion and our understanding of the sequence-structure relationship.
Altered functional connectivity in early Alzheimer's disease: A resting‐state fMRI study

Previous studies have led to the proposal that patients with Alzheimer's disease (AD) may have disturbed functional connectivity between different brain regions. Furthermore, recent resting‐state functional magnetic resonance imaging (fMRI) studies have also shown that low‐frequency (<0.08 Hz) fluctuations (LFF) of the blood oxygenation level‐dependent signals were abnormal in several brain areas of AD patients. However, few studies have investigated disturbed LFF connectivity in AD patients. By using resting‐state fMRI, this study sought to investigate the abnormal functional connectivities throughout the entire brain of early AD patients, and analyze the global distribution of these abnormalities. For this purpose, the authors divided the whole brain into 116 regions and identified abnormal connectivities by comparing the correlation coefficients of each pair. Compared with healthy controls, AD patients had decreased positive correlations between the prefrontal and parietal lobes, but increased positive correlations within the prefrontal lobe, parietal lobe, and occipital lobe. The AD patients also had decreased negative correlations (closer to zero) between two intrinsically anti‐correlated networks that had previously been found in the resting brain. By using resting‐state fMRI, our results supported previous studies that have reported an anterior–posterior disconnection phenomenon and increased within‐lobe functional connectivity in AD patients. In addition, the results also suggest that AD may disturb the correlation/anti‐correlation effect in the two intrinsically anti‐correlated networks. Hum Brain Mapp 2006. © 2006 Wiley‐Liss, Inc.
The self and recollective experience.

Three experiments investigated the hypothesis that self-reference at encoding increases the probability of recollective experience in recognition memory. In all three experiments separate groups of subjects studied words naming personality traits. One group judged the self-relevance of the traits, the other groups performed orientating tasks low in self-reference. In a recognition test subjects first identified old items and then indicated which of these were accompanied by recollective experience ('remember' responses) and which were recognized on some other basis ('know' responses). No reliable differences in overall recognition performance between self-referent and semantic encoding tasks were observed. However, subjects who encoded trait adjectives with reference to the self produced reliably more remember responses and few know responses than subjects who had encoded the items in the low self-referent tasks. Experiment 1 demonstrated a self-reference effect in recognition accompanied by recollective experience after 1-hour retention interval, while Experiment 2 found this effect to persist over a 24-hour retention interval. Experiment 3 demonstrated that this self-reference effect is obtained under incidental as well as under intentional learning conditions. Taken together these findings demonstrate the importance of self-reference as a factor in determining the likelihood that recognition judgements will be accompanied by recollective experience.
Telling the Secret

A questionnaire survey of 755 adults sexually abused as children, asking about the circumstances of their disclosure to the first person they told, resulted in 286 responses of which 228 were from female victims of incest. Individuals were asked basic demographic information, details about their abuse, who they first told, the reaction of the first person told, and reasons why they delayed telling or finally did tell. The women in this sample told in three groups. Those telling their parents first were likely to tell in childhood. A second group telling friends, other family members, or partners were more likely to tell in early adulthood. A third group, those telling therapists, revealed the abuse at a later age. Those revealing the incest to parents in childhood received a worse reaction than did those waiting until adulthood. When women disclosed to parents prior to age 18, the incest continued for more than a year after the disclosure in 51.9% of the cases. The women in this sample who disclosed as children were likely to be met with disbelief or blame rather than with support, validation, and protection.
CALL FOR PAPERS Integrative and Translational Physiology: Inflammation and Immunity in Organ System Physiology Disassociation of static and dynamic cerebral autoregulatory performance in healthy volunteers after lipopolysaccharide infusion and in patients with sepsis

Ronan M. G. Berg, Ronni R. Plovsing, Andreas Ronit, Damian M. Bailey, Niels-Henrik Holstein-Rathlou, and Kirsten Møller Centre of Inflammation and Metabolism, Department of Infectious Diseases, University Hospital Rigshospitalet, Copenhagen Ø, Denmark; Renal and Vascular Research Section, Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark; Intensive Care Unit 4131, University Hospital Rigshospitalet, Copenhagen Ø, Denmark; Department of Infectious Diseases, University Hospital Rigshospitalet, Copenhagen Ø, Denmark; Neurovascular Research Laboratory, Faculty of Health, Science and Sport, University of Glamorgan, South Wales, United Kingdom; and Neurointensive Care Unit, Department of Neuroanaesthesiology, University Hospital Rigshospitalet, Copenhagen Ø, Denmark
Attitudes and the experience of integration

This paper is an attempt to raise awareness to attitudinal research regarding integration by highlighting some of the less visible factors that may influence teachers' attitudes towards the integration of students with Down syndrome. I make no claims for the general application or representativeness of the statements, but I will claim that the following analysis will raise some challenging issues for further thinking.
The Impact of the National Essential Medicines Policy on Rational Drug Use in Primary Care Institutions in Jiangsu Province of China

Background: Essential medicine policy is a successful global health policy to promote rational drug use. The aim of this study was to evaluate the impact of the National Essential Medicines Policy (NEMP) on the rational drug use in primary care institutions in Jiangsu Province of China. Methods: In this exploratory study, a multistage, stratified, random sampling was used to select 3400 prescriptions from 17 primary care institutions who implemented the NEMP before (Jan 2010) and after the implementation of the NEMP (Jan 2014). The analyses were performed in SPSS 18.0 and SPSS Clementine client. Results: After the implementation of the NEMP, the percentage of prescribed EML (Essential Medicines List) drugs rose significantly, the average number of drugs per prescription and average cost per prescription were declined significantly, while the differences of the prescription proportion of antibiotics and injection were not statistically significant. BP (Back Propagation) neural network analysis showed that the average number of drugs per prescription, the number of using antibiotics and hormone, regional differences, size of institutions, sponsorship, financial income of institutions, doctor degree, outpatient and emergency visits person times were important factors affecting the prescription costs, among these the average number of drugs per prescription has the greatest effect. Conclusion: The NEMP can promote the rational use of drugs in some degree, but its role is limited. We should not focus only on the EML but also make comprehensive NEMP.
Belief in animal mind: does familiarity with animals influence beliefs about animal emotions?

Abstract Belief in the mental lives of nonhuman animals can have an impact on how we view and treat them, yet little is known about how and why laypeople attribute emotions to other species. The current study investigated how familiarity with animals (in terms of ownership) relates to beliefs regarding different emotions within and across species. An opportunity sample of 200 participants completed a questionnaire that measured familiarity with animals and beliefs about the capacity of a variety of species to experience a range of 16 different emotions. Participants reported varied levels of experience with animals and it was found that, regardless of familiarity, participants reported a wide variety of emotions in all the species they were asked to consider. However, participants who had never lived with an animal reported far fewer emotions than those who had, regardless of species. Keeping more than one animal did not increase the number of emotions reported. Keepers of a particular species always reported more emotions for that species than nonkeepers of that species. We conclude that familiarity with animals is an important determinant of belief about emotions in animals and animal mind in general.
Effect of litter quality on foot pad dermatitis, hock burns and breast blisters in broiler breeders during the production period

ABSTRACT Foot pad dermatitis and hock burn lesions are a form of contact dermatitis, a condition affecting skin areas in contact with unsuitable or irritating material. Contact dermatitis is a common problem, reducing the welfare of broilers, and is believed to also affect broiler breeders. However, there is very little research on contact dermatitis in breeders. This study followed the severity of foot pad lesions in broiler breeders throughout the production period. At slaughter the presence of hock burns and breast blisters was also determined. In addition, changes in litter condition over time and the impact of litter quality on foot pads were evaluated. The study was performed on 10 broiler breeder farms, including altogether 18 flocks. Foot pads of 100 hens per flock were assessed at the end of rearing period, three times during the production period, and at slaughter. Foot pad and hock lesions, as well as litter condition were scored on a 5-point scale. Litter quality was evaluated as pH, moisture and ammonia content. The condition of foot pads deteriorated towards slaughter age, with the occurrence of severe lesions reaching a maximum of 64% on average at slaughter. Hock lesions and breast blisters were rare. The litter layer became drier over time. Although poorer litter condition and wetness influenced foot pad health negatively, the effect on severe lesions was not significant. We also observed a negative effect on foot pad condition of larger slat areas. In conclusion, maintaining good litter quality alone is not enough to ensure healthy foot pads in broiler breeders.
Raw Speech Signal-based Continuous Speech Recognition using Convolutional Neural Networks

Abstract State-of-the-art automatic speech recognition systems model the relationship be-tween acoustic speech signal and phone classes in two stages, namely, extractionofspectral-basedfeaturesbasedonpriorknowledgefollowedbytrainingofacous-tic model, typically an articial neural network (ANN). In a recent work, it wasshownthatconvolutionneuralnetworks(CNNs)arecapableofmodelingtherela-tionbetweenacousticspeechsignalandphoneclassesdirectly. Thispaperextendsthe CNN-based approach to large vocabulary speech recognition task. More pre-cisely,wecomparetheCNN-basedapproachagainsttheconventionalANN-basedapproachonWallStreetJournalcorpus. OurstudiesshowthattheCNN-basedap-proachwithfewerparametersachievesperformancecomparableorbetterthantheconventional ANN-based approach. 1 Introduction State-of-the-art Automatic speech recognition (ASR) systems typically divide the task into severalsub-tasks, which are optimized in an independent manner [1]. In a rst step, the data is transformedinto features, usually composed of a dimensionality reduction phase and an information selectionphase, based on the task-specic knowledge of the phenomena. These two phases have been care-fully hand-crafted, leading to state-of-the-art features such as mel frequency cepstral coefcients(MFCCs) [2] or perceptual linear prediction cepstral features (PLPs) [3]. In a second step, the like-lihood of subword units such as, phonemes is estimated using generative models or discriminativemodels. In a nal step, dynamic programming techniques are used to recognize the word sequencegiven the lexical and syntactical constraints.Recent advances in machine learning have made possible systems that can be trained in an end-to-end manner, i.e. systems where every step islearned simultaneously, taking into account allthe other steps and the nal task of the whole system. It is typically referred to asdeep learning,mainly because such architectures are usually composed of many layers (supposed to provide anincreasing level of abstraction), compared to classical shallow systems. As opposed to divideand conquer approaches presented previously (where each step is independently optimized) deeplearning approaches are often claimed to have the potential to lead to more optimal systems, and tohave the advantage to alleviate the need of nd the right features for a given task of interest. Whilethere is a good success record of such approaches in the computer vision [4] or text processingelds [5], deep learning approaches for speech recognition still rely on spectral-based features suchas MFCC [6]. Some systems have proposed to learn features from intermediate representation ofspeech, like mel lter bank energies and their temporal derivatives.Inarecentstudy[7], itwasshownthatitispossibletoestimatephonemeclassconditionalprobabil-ities by using raw speech signal as input to convolutional neural networks [8] (CNNs). On TIMITphonemerecognitiontask, itwasshownthatthesystemisabletolearnfeaturesfromtherawspeech1
LASSO Isotone for High-Dimensional Additive Isotonic Regression

Additive isotonic regression attempts to determine the relationship between a multidimensional observation variable and a response, under the constraint that the estimate is the additive sum of univariate component effects that are monotonically increasing. In this article, we present a new method for such regression called LASSO Isotone (LISO). LISO adapts ideas from sparse linear modeling to additive isotonic regression. Thus, it is viable in many situations with high-dimensional predictor variables, where selection of significant versus insignificant variables is required. We suggest an algorithm involving a modification of the backfitting algorithm CPAV. We give a numerical convergence result, and finally examine some of its properties through simulations. We also suggest some possible extensions that improve performance, and allow calculation to be carried out when the direction of the monotonicity is unknown. Supplemental materials are available online for this article.
In Vivo Microdialysis Reveals Age-Dependent Decrease of Brain Interstitial Fluid Tau Levels in P301S Human Tau Transgenic Mice

Although tau is a cytoplasmic protein, it is also found in brain extracellular fluids, e.g., CSF. Recent findings suggest that aggregated tau can be transferred between cells and extracellular tau aggregates might mediate spread of tau pathology. Despite these data, details of whether tau is normally released into the brain interstitial fluid (ISF), its concentration in ISF in relation to CSF, and whether ISF tau is influenced by its aggregation are unknown. To address these issues, we developed a microdialysis technique to analyze monomeric ISF tau levels within the hippocampus of awake, freely moving mice. We detected tau in ISF of wild-type mice, suggesting that tau is released in the absence of neurodegeneration. ISF tau was significantly higher than CSF tau and their concentrations were not significantly correlated. Using P301S human tau transgenic mice (P301S tg mice), we found that ISF tau is fivefold higher than endogenous murine tau, consistent with its elevated levels of expression. However, following the onset of tau aggregation, monomeric ISF tau decreased markedly. Biochemical analysis demonstrated that soluble tau in brain homogenates decreased along with the deposition of insoluble tau. Tau fibrils injected into the hippocampus decreased ISF tau, suggesting that extracellular tau is in equilibrium with extracellular or intracellular tau aggregates. This technique should facilitate further studies of tau secretion, spread of tau pathology, the effects of different disease states on ISF tau, and the efficacy of experimental treatments.
A New Principle for Incremental Heuristic Search: Theoretical Results

Planning is often not a one-shot task because either the world or the agent's knowledge of the world changes. In this paper, we introduce a new principle that can be used to solve a series of similar search tasks faster with heuristic search methods than running individual searches in isolation, by updating the heuristics over time to make them more informed and thus future searches more focused. This principle is simple and easy to integrate into heuristic search methods, and it is easy to prove the correctness of the resulting heuristic search methods.
Survival of multiple myeloma patients in the era of novel therapies confirms the improvement in patients younger than 75 years: a population‐based analysis

Novel treatments for multiple myeloma (MM) have shown promising results in clinical trials, but the advantage in unselected patients is still unclear. In order to evaluate whether novel therapies impact survival of MM patients, we performed a population‐based analysis on data collected by the Modena Cancer Registry from 1989 to 2009. The analysis evaluated 1206 newly diagnosed MM patients collected in the years 1988–96 (conventional therapy), 1997–05 (high dose melphalan and autologous transplant), and 2006–09 (novel agents era). Both relative survival (RS) and overall survival (OS) improved over the years, but not equally in the three groups. For patients aged <65 years, RS improved in 1997–05 and 2006–09 compared with previous years and a trend to improvement was observed from 1997–05 to 2006–09. For patients aged 65–74 years, RS improved significantly in 2006–09 compared with 1988–96 and 1997–05. No amelioration was observed for patients 75+ years old. OS confirmed RS. In conclusion, the survival of MM patients aged <65 and, in particular, 65–74 years, has improved over time, especially after 2006. This observation provides circumstantial evidence that novel therapies might impact patient survival. Despite the limits of this study, these data refer to an unselected population, giving a picture of every day clinical practice.
Vasodilatory response of border zones to acetazolamide before and after endarterectomy : an echo planar imaging-dynamic susceptibility contrast-enhanced MRI study in patients with high-grade unilateral internal carotid artery stenosis.

BACKGROUND AND PURPOSE The importance of hemodynamic changes related to a high-grade internal carotid artery (ICA) stenosis remains a matter of controversy. Areas between the vascular territories of major cerebral arteries, namely, the border zones, may be selectively vulnerable to hemodynamic alteration. The aim of this study was to search for any hemodynamic impact of carotid endarterectomy (CEA) on vasodilatory response, in particular, within the border zones, by means of multislice dynamic susceptibility contrast MRI. METHODS Thirteen patients with a high-grade unilateral ICA stenosis (>80%) were examined. Relative regional cerebral blood volume (rrCBV) was determined separately for white matter, gray matter, and anterior and posterior border zones by the acetazolamide test. A vasomotor reactivity index was evaluated from the rrCBV values. Values from the ipsilateral hemisphere were compared with contralateral ones, before and after CEA. RESULTS Before CEA, rrCBV values in the anterior border zones were significantly (P<0.05) higher in the ipsilateral hemisphere than in the contralateral hemisphere. A decrease in vasomotor reactivity indexes was also observed in the lesion side, but the difference from the contralateral side was not statistically significant. In posterior border zones, no differences in rrCBV or vasomotor reactivity were found between the ipsilateral and the contralateral hemispheres. After CEA, the rrCBV asymmetry in the anterior border zones cleared. CONCLUSIONS High-grade ICA stenosis with efficient primary collateral pathways may have an early limited hemodynamic impact within border-zone areas. The favorable course of these abnormalities after surgery suggests an additional benefit of CEA at this stage.
Development and test of a model of external organizational commitment in human resources outsourcing

Most prior outsourcing studies in the human resources domain have focused on the initial decision for outsourcing HR activities. Hence, little is known about HR managers' commitment to continue an already existing outsourcing relationship. This study constitutes a first step to increase our understanding of the factors related to the continuity of HR outsourcing relationships. We developed and tested a model of HR managers' (N = 186) commitment in outsourcing relationships. Affective commitment or the desire for the outsourcing relationship to continue was related to the depth and frequency of HR outsourcing. Conversely, continuance commitment, which refers to the constraints that keep the outsourcing relationship intact, was not related to the continuity of HR outsourcing. Finally, affective commitment was fostered by HR managers' perception that HR vendors shared the same values for managing people. © 2008 Wiley Periodicals, Inc.