Miracle-dz/UniFAR-FTUs huggingface dataset:
Biases in research: risk factors for non-replicability in psychotherapy and pharmacotherapy research

Replicability of findings is an essential prerequisite of research. For both basic and clinical research, however, low replicability of findings has recently been reported. Replicability may be affected by research biases not sufficiently controlled for by the existing research standards. Several biases such as researcher allegiance or selective reporting are well-known for affecting results. For psychotherapy and pharmacotherapy research, specific additional biases may affect outcome (e.g. therapist allegiance, therapist effects or impairments in treatment implementation). For meta-analyses further specific biases are relevant. In psychotherapy and pharmacotherapy research these biases have not yet been systematically discussed in the context of replicability. Using a list of 13 biases as a starting point, we discuss each bias's impact on replicability. We illustrate each bias by selective findings of recent research, showing that (1) several biases are not yet sufficiently controlled for by the presently applied research standards, (2) these biases have a pernicious effect on replicability of findings. For the sake of research credibility, it is critical to avoid these biases in future research. To control for biases and to improve replicability, we propose to systematically implement several measures in psychotherapy and pharmacotherapy research, such as adversarial collaboration (inviting academic rivals to collaborate), reviewing study design prior to knowing the results, triple-blind data analysis (including subjects, investigators and data managers/statisticians), data analysis by other research teams (crowdsourcing), and, last not least, updating reporting standards such as CONSORT or the Template for Intervention Description and Replication (TIDieR).
The Number and Observability of Population III Supernovae at High Redshifts

We consider the feasibility of detecting Population III pair-instability supernovae (PISNe) at very high redshifts with the James Webb Space Telescope (JWST). Four published estimates for the PISN rate show a rather wide dispersion, between 50 and 2200 deg-2 yr-1. Correcting problems with several of these, we conclude that even a fairly optimistic estimate is probably a further order of magnitude lower than this range, at a rate of the order of 4 deg-2 yr-1 at z ~ 15 and 0.2 deg-2 yr-1 at z ~ 25, both with substantial uncertainty. Although such supernovae (SNe) would be bright enough to be readily detectable with the JWST at any relevant redshift, the lower number densities derived here would likely require either a dedicated wide-angle search strategy or a serendipitous search. We expect that typically about 1 deg2 (or 500 JWST NIRCam images) at 4.5 μm must be imaged to detect one PISN at z ~ 15 and about 35 deg2 to detect one at z ~ 25. If some Population III star formation persists to lower redshifts at z ~ 5, then PISNe may also be detectable in wide-angle ground-based Z-band imaging surveys at ZAB ~ 23, at a density of the order of 1 deg-2 of surveyed area. In the Appendix we consider the possible effects of intergalactic dust in obscuring high-redshift SNe or other high-redshift sources. We show that the obscuration at a given rest wavelength will peak at some maximum redshift and thereafter decline. While it may be a significant effect in observations of the very high redshift universe, it is unlikely, even under rather pessimistic assumptions, to completely obscure primordial objects.
Modelling the initial spread of foot-and-mouth disease through animal movements

Livestock movements in Great Britain (GB) are well recorded and are a unique record of the network of connections among livestock-holding locations. These connections can be critical for disease spread, as in the 2001 epidemic of foot-and-mouth disease (FMD) in the UK. Here, the movement data are used to construct an individual-farm-based model of the initial spread of FMD in GB and determine the susceptibility of the GB livestock industry to future outbreaks under the current legislative requirements. Transmission through movements is modelled, with additional local spread unrelated to the known movements. Simulations show that movements can result in a large nationwide epidemic, but only if cattle are heavily involved, or the epidemic occurs in late summer or early autumn. Inclusion of random local spread can considerably increase epidemic size, but has only a small impact on the spatial extent of the disease. There is a geographical bias in the epidemic size reached, with larger epidemics originating in Scotland and the north of England than elsewhere.
Post-traumatic stress disorder in parents of children hospitalized in the neonatal intensive care unit (NICU): medical and demographic risk factors.

BACKGROUND Post-traumatic stress disorder (PTSD) among parents of neonates hospitalized in the Neonatal Intensive Care Units (NICU) stays an underestimated problem. We determined the incidence of PTSD in parents and pointed out medical and demographic risk factors for PTSD in neonates hospitalized in the NICU. SUBJECT AND METHODS The study involved 39 mothers and 27 fathers of 42 infants aged 1 to 16 months who were hospitalized in the NICU of a Children's University Hospital during the neonatal period. As a measure of PTSD we used the Polish version of the Impact of Event Scale-Revised (IES-R). The current level of stress was measured using the Perceived Stress Scale (PSS-10). The author's questionnaire contained demographic and medical information on the infants hospitalized in the NICU and their parents. Data were statistically analyzed. RESULTS The incidence of PTSD and levels of stress did not differ in the group of mothers and fathers. There was a statistically significant difference in the severity of PTSD symptoms in general (p=0.006) and the severity of symptoms of intrusion (p=0.009) and arousal (p=0.015), which were more pronounced in mothers of children hospitalized in the NICU than in their fathers. In the multivariate models perceived stress was the only predictor that significantly affected the rate of PTSD symptoms in parents. CONCLUSIONS Since PTSD is a very common problem in parents of children hospitalized in the NICU and estimating the risk of its occurrence on the basis of collected data is not possible, the parents of all those children should be considered at high risk.
The mysterious RAMP proteins and their roles in small RNA‐based immunity

A new class of prokaryotic RNA binding proteins called Repeat Associated Mysterious Proteins (RAMPs), has recently been identified. These proteins play key roles in a novel type immunity in which the DNA of the host organism (e.g. a prokaryote) has sequence segments corresponding to the sequences of potential viral invaders. The sequences embedded in the host DNA confer immunity by directing selective destruction of the nucleic acid of the virus using an RNA‐based strategy. In this viral defense mechanism, RAMP proteins have multiple functional roles including endoribonucleotic cleavage and ribonucleoprotein particle assembly. RAMPs contain the classical RNA recognition motif (RRM), often in tandem, and a conserved glycine‐rich segment (G‐loop) near the carboxyl terminus. However, unlike RRMs that bind single‐stranded RNA using their β‐sheet surface, RAMPs make use of both sides of the RRM fold and interact with both single‐stranded and structured RNA. The unique spatial arrangement of the two RRM folds, facilitated by a hallmark G‐loop, is crucial to formation of a composite surface for recognition of specific RNA. Evidence for RNA‐dependent oligomerization is also observed in some RAMP proteins that may serve as an important strategy to increase specificity.
NONLINEAR APPROXIMATION AND THE SPACE BV ( R 2 ) By

Given a function f 2 L2(Q), Q := [0, 1)2 and a real number t > 0, let U( f , t) := infg2BV (Q) kf gkL2(I) + t VQ (g), where the infimum is taken over all functions g 2 BV of bounded variation on I. This and related extremal problems arise in several areas of mathematics such as interpolation of operators and statistical estimation, as well as in digital image processing. Techniques for finding minimizers g for U( f , t) based on variational calculus and nonlinear partial differential equations have been put forward by several authors [DMS], [RO], [MS], [CL]. The main disadvantage of these approaches is that they are numerically intensive. On the other hand, it is well known that more elementary methods based on wavelet shrinkage solve related extremal problems, for example, the above problem with BV replaced by the Besov space B1(L1(I)) (see e.g. [CDLL]). However, since BV has no simple description in terms of wavelet coefficients, it is not clear that minimizers for U( f , t) can be realized in this way. We shall show in this paper that simple methods based on Haar thresholding provide near minimizers for U( f , t). Our analysis of this extremal problem brings forward many interesting relations between Haar decompositions and the space BV.
Enhance Trust based Routing Techniques against Sinkhole Attack in AODV based VANET

network is a collection of wireless nodes communicating among themselves over multihop paths, without the help of any infrastructure such as base stations or access points. Vehicular Ad-hoc Networks (VANETs) are self-organizing, self-configuring confederation of wireless systems. At present, vehicular networks are still not considered to be very efficient because of their rapid topology changes and their highly dynamic structure. The Vehicular Ad-hoc Networks security attack is a challenging job. A new routing protocol based on the trust model is proposed and analysed in this paper. Here each node calculates trust value and association status for all its neighboring nodes through monitoring its behavior in the network. The trust model is integrated into the Adhoc on-demand distance vector routing (AODV) protocol which is the most common on demand routing protocol used in VANET. In the proposed scheme the route is not selected on the basis of first arrival of Route Reply and waits till it gets the Route Reply from all neighboring nodes and decides the path to be routed based on the nature of Association between them. Thus the Sinkhole nodes will be identified and will not be given preference in the route selection. The performance the proposed protocol is evaluated by comparing the Ns-2 simulation results of it with Standard AODV in presence of Sinkhole nodes. The simulation results demonstrate.
Human Embryonic Stem Cells as a Model for Studying Epigenetic Regulation During Early Development

In order to exploit the exceptional potential of human embryonic stem cells (hESCs) incell-replacement therapies, the genetic and epigenetic factors controlling early humandevelopment must be better defined. Limitations in human embryonic material restrict thescale of studies that can be performed, and therefore an in vitro model in which to studyepigenetic regulation in human pre-implantation cell types would be desirable. HESCscould provide such a model, but since they are derived from a stage in mammaliandevelopment when the genome is undergoing global epigenetic remodelling, it is unclearwhether their epigenetic status would be stable or subject to variation. Herein, we discussrecent work that examines allele-specific imprinted gene expression and methylationpatterns, thereby demonstrating that hESCs maintain a substantial degree of epigeneticstability during culture. Therefore, we suggest that hESCs could provide a model forstudying epigenetic regulation during the early stages of human cellular pluripotency anddifferentiation. Furthermore, we propose specific experiments using such a model toaddress important questions pertaining to epigenetic mechanisms of certain humandisorders.
Automated Analysis of Security Protocols with Global State

Security APIs, key servers and protocols that need to keep the status of transactions, require to maintain a global, non-monotonic state, e.g., in the form of a database or register. However, existing automated verification tools do not support the analysis of such stateful security protocols - sometimes because of fundamental reasons, such as the encoding of the protocol as Horn clauses, which are inherently monotonic. An exception is the recent tamarin prover which allows specifying protocols as multiset rewrite (MSR) rules, a formalism expressive enough to encode state. As multiset rewriting is a "low-level" specification language with no direct support for concurrent message passing, encoding protocols correctly is a difficult and error-prone process. We propose a process calculus which is a variant of the applied pi calculus with constructs for manipulation of a global state by processes running in parallel. We show that this language can be translated to MSR rules whilst preserving all security properties expressible in a dedicated first-order logic for security properties. The translation has been implemented in a prototype tool which useqs the tamarin prover as a backend. We apply the tool to several case studies among which a simplified fragment of PKCS#11, the Yubikey security token, and an optimistic contract signing protocol.
WCDMA multi-cell link-level performance

This paper presents a multi-cell simulation approach with which the impact of selected link-level aspects on cellular system performance can be investigated. The investigations are carried out for downlink dedicated physical channels (DL-DPCH) of third-generation wideband CDMA (3G WCDMA), specified by the 3GPP standardization body. The simulator incorporates user equipment (UE) that suffers from intra-cell interference of the connected base station (BS) as well as inter-cell interference originating from explicitly, i.e. chip-exact, modeled surrounding BSs. The employed multi-cell environment, based on a radio geometry concept; is described. Coded error performance is shown for various mobile radio channel scenarios, radio geometries and different models for the interference. The question whether inter-cell interference of surrounding BSs can be modeled alternatively by additive white Gaussian noise (AWGN) is addressed. It turns out that in all cases the chip-exact modelling of adjacent BSs is necessary in order to obtain realistic performance results. This holds especially the more the UE moves towards the cell border and beyond. Comparisons with simulations employing the AWGN model for inter-cell interference show that those results are too optimistic at low speeds. Moreover, it is shown that a performance analysis based solely on uncoded (raw) bit error rate is not sufficient, but must be complemented by decoded bit and block error rate figures.
The relationship between infant peer interactions and cognitive development: Evidence from rural China

Social interactions in infancy have implications for long-term outcomes. This study uses data from a sample of 1412 rural Chinese infants aged 6–12 and 24–30 months to examine the relationship between peer interactions and cognitive development. Over 75% of the infants in this sample had less than three peers and around 20% had no peers in both periods. The prevalence of cognitive delays is high within this sample and increases as infants age. Multivariate analysis reveals that peer interaction is significantly associated with cognitive development. Heterogeneous analysis suggests that peer interactions and mental development may be related to the child’s primary caregiver and the distance from the child’s household to the center of their village.
The effect of type and level of protein, fibre and starch on nitrogen excretion patterns in rats

1. Three series of nitrogen balance experiments were performed with growing rats to test the effect of type and level of protein, fibre and starch on N excretion patterns. The design involved eighteen treatments in a 3×3×2 factorial experiment with five rats per dietary treatment. The eighteen treatments resulted from a combination of three protein treatments, three fibre treatments and two starch treatments. Protein treatments consisted of onelevel (15 g N/kg DM) of casein fortified with methionine, a protein of high digestibility, and two levels (15 and 20 g N/kg DM) of autoclaved brown beans (Phaseolus vulgaris), a protein source of low digestibility. The fibre treatments were two levels of cellulose powder and one level of barley hulls. The two starch treatments were autoclaved potato starch and autoclaved and raw potato starch (1:1, w/w). 2. The inclusion of raw potato starch reduced true protein digestibility markedly when the protein source was casein, but the corresponding biological values were increased significantly with this treatment. This strongly indicated a movement of urea from the blood to the intestines. This assumption was also supported by significantly lower blood urea concentrations in animals given raw starch. The influence of raw starch on true protein digestibility was, however, significantly less when cellulose and barley hulls were included. This is probably due to reduced transit time from fibre inclusion. The nature of the gut contents also supported this hypothesis. 3. The inclusion of raw potato starch when brown beans were the source of protein had much less effect on true protein digestibility and biological value than when casein was the protein source. This was probably due to the low digestibility of DM and protein in this food leaving sufficient energy and protein for maximum microbial growth. The inclusion of fibre also had little effect on N excretion patterns with the brown-bean diets. 4. An increase in the level of brown bean inclusion reduced true protein digestibility only on the diets containing raw starch whereas the biological value was consistently reduced regardless of starch treatment. The lower biological values were associated with significantly higher blood urea concentrations. Increasing the level of brown bean inclusion also resulted in higher fresh weights of caecum, colon and contents. 5. The present work proves that, through dietary manipulation, it is possible to affect nitrogen excretion patterns in rats.
Rule-Based versus Associative Processes in Derivational Morphology

The present article examines whether derivational morphology shows evidence of an associative memory structure. A distributional analysis of stems of attested derivational forms revealed evidence of clustering around phonological properties (gangs) for all nonneutral affixes but only a few neutral affixes. Subjects' acceptability ratings for novel complex words revealed sensitivity to the gang structure associated with the relevant derivational affixes. Results suggest that, like inflectional morphology, derivational morphology shows dissociations between rule-based and associative generalization mechanisms.
Glass as a nonlinear optical material

Interest in nonlinear optics has been growing rapidly. Today many materials are known to possess nonlinear effects and the intense search for even more efficient and cost-effective materials is continuing. Various crystals are known for large nonlinear coefficients however their limitations in size and high cost make other solid state materials such as glass more attractive despite their relatively smaller non-linear coefficients. We review the research on glasses with high nonlinearity by classifying them into homogenous type and heterogeneous type. 1.
Statistical adaptation of acoustic models to noise conditions for robust speech recognition

Noise degrades the performance of Automatic Speech Recognition (ASR) systems working in real condition. The mismatch between the training and recognition conditions is considered the main factor involved in this degradation, and most methods for robust ASR are focussed on its minimization. In this work, we compare robust methods for ASR based on (a) the compensation of the noise effects and (b) the adaptation of the acoustic models to noise con-ditions. We propose a method for the adaptation of the acoustic models to the noise conditions based on a statistical formulation. In this method, each Gaussian is adapted to the noisy environment according to the estimated noise conditions. Recognition experiments have been carried out using speech acquired in real car environments. The results show the statistical formulation for adaptation provides an accurate method for robust ASR.
Testing evidence of recent hydration state change in sulfates on Mars

The East Candor Interior Layered Deposit (ILD) has signatures of mono‐ and polyhydrated sulfate in alternating layers that give insight into the processes which formed these layered deposits and on the environmental conditions acting on them since then. We use orbital data to explore multiple hypotheses for how these deposits formed: (1) sulfate‐bearing ILDs experience hydration changes on seasonal to a few years timescales under current Mars environmental conditions; (2) the deposits experience hydration under recent Mars conditions but require the wetter climate of high obliquity; and (3) the kieserite could be an original or diagenetic part of a complex evaporite mineral assemblage. Modeled climatology shows recent Mars environmental conditions might pass between multiple sulfate fields. However, comparison of Observatoire pour la Mineralogie, l'Eau, les Glaces et l'Activite (OMEGA) and Compact Reconnaissance Imaging Spectrometer (CRISM) observations of the same ILD do not show changes in hydration over 2 Mars years. Low temperatures might slow the kinetics of that transition; it is likely that more clement conditions during periods of high obliquity are needed to overcome mineral metastability and hydrate kieserite‐bearing deposits. We find the alternate model, that the deposit is a cyclic evaporite sequence of mono‐ and polyhydrated sulfates, also plausible but with an unexplained dearth of Fe sulfates.
Learning Articulated Skeletons from Motion

Humans demonstrate a remarkable ability to parse complicated motion sequences into their constituent structures and motions. We investigate this problem, attempting to learn the structure of one or more articulated objects, given a time-series of feature positions. We model the observed sequence in terms of “stick figure” objects, under the assumption that the relative joint angles between sticks can change over time, but their lengths and connectivities are fixed. We formulate the problem in a single probabilistic model that includes multiple sub-components: associating the features with particular sticks, determining the proper number of sticks, and finding which sticks are physically joined. We test the algorithm on challenging 2D and 3D datasets including optical human motion capture and video of walking giraffes.