Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive Functional Classification/Identification of Prokaryotic Transmembrane Proteins by Sequence and Topology Similarities

About one fourth of genes in genomes has been known to encode transmembrane (TM) proteins (TMPs) [2, 6, 8]. Although TMPs have important functions playing an essential role in life, detailed and comprehensive analysis of their functions haven’t been carried out yet. In this study, we tried to develop a novel method to classify and identify TMP functions with use of TM topology similarity in addition to sequence similarity. This idea is based on the recent finding that function of TMPs is closely correlated to their TM topology (a combination of short and long loops: topology pattern) and the function can be inferred from knowing the topology pattern [9]. By applying the TM topology similarity to the procedure of TMP functional classification/identification, it is expected to give functional annotations to the TMPs that cannot be annotated by sequence similarity.
A multiagent architecture for concurrent reinforcement learning

In this paper we propose a multiagent architecture for implementing concurrent reinforcement learning, an approach where several agents, sharing the same environment, perceptions and actions, work towards one only objective: learning a single value function. We present encouraging experimental results derived from the initial phase of our research on the combination of concurrent reinforcement learning and learning from demonstration.
IONOSPHERIC EFFECTS OF SEVERE GEOMAGNETIC STORMS

Earth’s ionosphere responds dramatically to severe geomagnetic storms. Coupled closely to the neutral thermosphere and the overlying magnetosphere, stormtime ionospheric effects appear with a wide variety of scale sizes, characteristics, time histories, and associated drivers. The strong interconnection between the magnetosphere and ionosphere points to the need to take a global perspective in characterizing and understanding this system. Penetrating electric fields and plasma redistribution combine to produce severe enhancements and reductions of ionospheric TEC (total electron content), steep localized density gradients, and stormtime space weather effects. 5.1.
Online Pair-Programming for Learning Programming of Novices

The purpose of this study is to determine the effects of online pair programming for novices. This paper describes two system designs for online pair programming: real-time synchronous pair programming and non-real-time asynchronous pair programming. An experiment was conducted to test the feasibility of online pair programming, using Squeak eToys as an educational programming language. Nebraska of Squeak eToys, a toolkit for building remote interactions with morphic (object-oriented and visual) projects in Squeak eToys, was used for sharing learners' screens and input devices, such as the keyboard and mouse. In this experiment, the following were compared: co-located pair programming, distributed pair programming, and individual programming, through the statistical analysis of their task scores; and a number of creative ideas and their scores in the final test, using T-test, ANOVA F-test, and post-comparison. The results showed that distributed pair programming is not significantly different from co-located pair programming, and that pair programming is more effective than individual programming. In addition, based on the students' sentiments and class observations, several suggestions are given herein, such as environments or teaching methods in online pair programming. The importance of communication, authority control, and peer pressure in online pair programming is also discussed in this paper. In conclusion, the results of this experimental research show that educators can be helped in designing effective learning systems for online pair programming.
Random Positive-Only Projections: PPMI-Enabled Incremental Semantic Space Construction

We introduce positive-only projection (PoP), a new algorithm for constructing semantic spaces and word embed-dings. The PoP method employs random projections. Hence, it is highly scalable and computationally efﬁcient. In contrast to previous methods that use random projection matrices R with the expected value of 0 (i.e., E ( R ) = 0 ), the proposed method uses R with E ( R ) > 0 . We use Kendall ’s τ b correlation to compute vector similarities in the resulting non-Gaussian spaces. Most importantly, since E ( R ) > 0 , weighting methods such as positive pointwise mutual information (PPMI) can be applied to PoP-constructed spaces after their construction for ef-ﬁciently transferring PoP embeddings onto spaces that are discriminative for semantic similarity assessments. Our PoP-constructed models, combined with PPMI, achieve an average score of 0.75 in the MEN relatedness test , which is comparable to results obtained by state-of-the-art algorithms.
Familial occurrence of psoriatic arthritis.

Although the association between psoriasis and arthritis has been known since the original description by Alibert (1818), it is only recently that the condition has become widely acknowledged as a disease sui generis (Vilanova and Pifiol, 1951; Coste, Franqon, Touraine, and Loyau, 1958; Wright, 1959). The general acceptance of the disorder stems largely from epidemiological (Baker, 1965), clinical (Wright, 1956, 1961; Baker, Golding, and Thompson, 1963a), and radiological (Avila, Pugh, Slocumb, and Winkelmann, 1960) data reported over the last decade. Despite this advance in our knowledge of psoriatic arthritis, the cause of the disorder remains unknown, but several recent studies have suggested that genetic factors may be important in aetiology (Tiedemann, 1951; Baker, Golding, and Thompson, 1963b; Theiss, B6ni, Wagenhauser, Schnyder, and Fehr, 1969a; Theiss, Schnyder, Boni, and Wagenhauser, 1969b; Theiss, Schnyder, and Boni, 1970). In order to examine further the importance of heredity in this disease, a large controlled family survey of probands with psoriatic arthritis has been undertaken at Leeds over a 2-year period. It is the purpose of this paper to report the major findings of this study. Clinical material
A Statistical Model for Expression Generation using the Facial Action Coding System

We demonstrate a novel method of automatically generating facial expressions from still images of faces. Human-computer interaction would greatly benefit from automatic facial expression generation as arbitrary images of faces could be used to govern many applications. This new technique is a hybrid of Ekmans [19] Facial Action Coding System (FACS) and Cootes [10,11,16] Active Appearance Model (AAM). The FACS system is based on an anatomical analysis of facial muscles and the AAM is a statistical model of shape and texture based on faces used during a training phase. This method along with the correct warping procedure enhances the accuracy of the generated facial expressions. We describe the technique in detail and give results that suggest that the technique is feasible. We anticipate that this new technique will be used to automatically generate facial expressions in many applications.
Bidirectional Control of Postsynaptic Density-95 (PSD-95) Clustering by Huntingtin*

Background: Wild-type huntingtin (HTT) interacts with synaptic proteins, yet its role in synaptic function is unclear. Results: HTT bidirectionally influences PSD-95 clustering in striatal spiny projection neurons. Conclusion: HTT plays a role in synaptic protein organization. Significance: HTT-reducing strategies are being tested as a treatment for Huntington disease. It is therefore critical to understand the role of HTT in cellular and synaptic function. Huntington disease is associated with early alterations in corticostriatal synaptic function that precede cell death, and it is postulated that ameliorating such changes may delay clinical onset and/or prevent neurodegeneration. Although many of these synaptic alterations are thought to be attributable to a toxic gain of function of the mutant huntingtin protein, the role that nonpathogenic huntingtin (HTT) plays in synaptic function is relatively unexplored. Here, we compare the immunocytochemical localization of a major postsynaptic scaffolding protein, PSD-95, in striatal neurons from WT mice and mice overexpressing HTT with 18 glutamine repeats (YAC18, nonpathogenic). We found that HTT overexpression resulted in a palmitoylation- and BDNF-dependent increase in PSD-95 clustering at synaptic sites in striatal spiny projection neurons (SPNs) co-cultured with cortical neurons. Surprisingly, the latter effect was mediated presynaptically, as HTT overexpression in cortical neurons alone was sufficient to increase PSD-95 clustering in the postsynaptic SPNs. In contrast, antisense oligonucleotide knockdown of HTT in WT co-cultures resulted in a significant reduction of PSD-95 clustering in SPNs. Notably, despite these bidirectional changes in PSD-95 clustering, we did not observe an alteration in basal electrophysiological measures of AMPA and NMDA receptors. Thus, unlike in previous studies in the hippocampus, enhanced or decreased PSD-95 clustering alone was insufficient to drive AMPA or NMDA receptors into or out of SPN synapses. In all, our results demonstrate that nonpathogenic HTT can indeed influence synaptic protein localization and uncover a novel role of HTT in PSD-95 distribution.
Misresponse to Survey Questions: A Conceptual Framework and Empirical Test of the Effects of Reversals, Negations, and Polar Opposite Core Concepts

The authors propose a conceptual framework of misresponse to multi-item scales in surveys in which misresponse to items that are reversed relative to other items (reversal misresponse) is differentiated from misresponse to items that are negated (negation misresponse) and from misresponse to items whose core concept is the opposite of the core concept in regular items (polar opposite misresponse). The framework specifies two broad mechanisms to account for the three forms of misresponse: lack of motivation to process items in detail (“inattention”) and lack of ability to comprehend items accurately (“difficulty”). The authors propose a procedure to identify potential misresponse effects on the observed item responses and factor loadings, and they report two empirical studies to test the framework; the second study uses eye movement recordings to examine the underlying process. The findings reveal that polar opposite, reversed, and negated items contribute to misresponse to varying degrees and that difficulty rather than inattention may be a more potent cause of misresponse in surveys than has traditionally been acknowledged.
Impact of space-time block codes on 802.11 network throughput

By employing more than one antenna at the transmitter and by properly coding data across the transmit antennas, physical layers (PHYs) with space-time block codes (STBCs) promise increased data rates with minimal decoding complexity at the receiver. This paper presents a comprehensive study of how the STBC gains at the PHY translate to significant network performance improvement in 802.11a wireless local area networks. We base our study on a detailed, across-all-layers, simulation of an 802.11a system. We have extended the network simulator with an implementation of the 802.11a PHY, which allows us to assess the impact of STBC not only at the PHY layer, but at the higher layers as well. An extensive set of simulations illustrates the merits of transmit diversity (in the form of STBC) and sheds light on how performance can be improved for transmission control protocol (TCP) traffic. Essentially, STBC presents to TCP a "smoother" wireless channel; this is corroborated by a brief theoretical analysis as well.
Functional Comparison between Genes Dysregulated in Ulcerative Colitis and Colorectal Carcinoma

Background Patients with ulcerative colitis (UC) are predisposed to colitis-associated colorectal cancer (CAC). However, the transcriptional mechanism of the transformation from UC to CAC is not fully understood. Methodology Firstly, we showed that CAC and non-UC-associated CRC were very similar in gene expression. Secondly, based on multiple datasets for UC and CRC, we extracted differentially expressed (DE) genes in UC and CRC versus normal controls, respectively. Thirdly, we compared the dysregulation directions (upregulation or downregulation) between DE genes of UC and CRC in CRC-related functions overrepresented with the DE genes of CRC, and proposed a regulatory model to explain the CRC-like dysregulation of genes in UC. A case study for “positive regulation of immune system process” was done to reveal the functional implication of DE genes with reversal dysregulations in these two diseases. Principal Findings In all the 44 detected CRC-related functions except for “viral transcription”, the dysregulation directions of DE genes in UC were significantly similar with their counterparts in CRC, and such CRC-like dysregulation in UC could be regulated by transcription factors affected by pro-inflammatory stimuli for colitis. A small portion of genes in each CRC-related function were dysregulated in opposite directions in the two diseases. The case study showed that genes related to humoral immunity specifically expressed in B cells tended to be upregulated in UC but downregulated in CRC. Conclusions The CRC-like dysregulation of genes in CRC-related functions in UC patients provides hints for understanding the transcriptional basis for UC to CRC transition. A small portion of genes with distinct dysregulation directions in each of the CRC-related functions in the two diseases implicate that their reversal dysregulations might be critical for UC to CRC transition. The cases study indicates that the humoral immune response might be inhibited during the transformation from UC to CRC.
Virulence Factors Contributing to Pathogenicity of Candida tropicalis and Its Antifungal Susceptibility Profile

The incidence of invasive candidiasis has increased over the past few decades. Although Candida albicans remains by far the most common species encountered, in recent years shift towards non-albicans Candida species like Candida tropicalis is noted. Here in this study we determined the virulence factors and antifungal susceptibility profile of 125 C. tropicalis isolated from various clinical specimens. Biofilm formation was seen in 53 (42.4%) isolates. Coagulase production was noted in 18 (14.4%) isolates. Phospholipase enzyme was the major virulent factor produced by C. tropicalis isolates. A total of 39 biofilm forming isolates showed phospholipase activity. Proteinase activity was demonstrated by 65 (52%) isolates. A total of 38 (30.4%) isolates showed haemolytic activity. Maximum isolates demonstrated resistance to fluconazole. Fluconazole resistance was more common in C. tropicalis isolated from blood cultures. Antifungal resistance was more in isolates possessing the ability to produce phospholipase and biofilm. C. tropicalis exhibit a great degree of variation not only in their pathogenicity but also in their antifungal susceptibility profile. The identification of virulence attributes specific for each species and their correlation with each other will aid in the understanding of the pathogenesis of infection.
Evaluating the Effect of Absolute and Barometric Pressures on Borehole Performance in Tolon and Wa West Districts of Northern Ghana

Groundwater is a very important asset to the people of Northern Ghana where majority are farmers as its used for many domestic and agricultural activities. The research evaluated the effects of absolute and barometric pressures on water-table fluctuations of boreholes in Wa West and Tolon Districts of Northern Ghana. Pumping tests, absolute and barometric pressures were monitored using non-vented water level sensors for one year, from 2015-2016. The results of the research indicate that, the aquifer of the Kpaligung borehole is of Voltaian province while that of Baleofili is Granitoid intrusions. The yield of the Baleofili borehole is 1.8 m3/h (30 l/min), while that of the Kpaligung borehole yields 1.4 m3/h (23 l/min). Rainfall regime has considerable effects on Kpaligung and Baleofili boreholes` recharge and water-table fluctuation due to the effects of both absolute and barometric pressure throughout the year. The relationship between barometric pressure and water pressure for the Kpaligung borehole shows positive, but weak correlation value (0.2) that is, increase in barometric pressure leads to an increase in water level and vice versa. The Baleofili borehole shows an inverse relationship between barometric pressure and water level pressure with the coefficient of correlation being 0.5. The relationship between the changes in water level of the boreholes with the corresponding change in rainfall amount suggests that the groundwater recharge of the boreholes depends considerably on annual rainfall variation in the study areas considered.
Money, Sex and Broken Promises: Politicians’ Bad Behaviour Reduces Trust

This article develops and tests empirically a theory of the effect on political trust of forms of behaviour that violate social, political and legal norms about how politicians ought to behave. These include taking money for favours, over-indulging in private life and making misleading promises to win votes. The evidence comes from a specially designed survey in Britain, France and Spain, countries where popular distrust of politicians appears greater than illegal political behaviour. Bad behaviours, especially abandoning election promises once in office, have a much stronger effect on distrust of political parties that do differences in partisanship. Comparing national regressions shows that the impact of bad behaviours is very similar in Britain, France and Spain.
Designing motion-based activities to engage students with autism in classroom settings

We report on a nine-month-long observational study with teachers and students with autism in a classroom setting. We explore the impact of motion-based activities on students' behavior. In particular, we examine how the playful gaming activity impacted students' engagement, peer-directed social behaviors, and motor skills. We document the effectiveness of a collaborative game in supporting initiation of social activities between peers, and in eliciting novel body movements that students were not observed to produce outside of game play. We further identify the positive impact of game play on overall classroom engagement. This includes an "audience effect" whereby non-playing peers direct initiations to those playing the game and vice versa, and a positive "spillover" effect of the activity on students' social behavior outside of game play. We identify key considerations for designing and deploying motion-based activities for children with autism in a classroom setting.
Eosinophilic esophagitis: Food impaction as a diagnostic prompt

Editor: Although the most common factors related to food impaction are gastroesophageal reflux, esophageal stricture, and Schatzki’s ring, we would briefly like to remind our colleagues that such an event, although not unusual, may represent as the initial manifestation of eosinophilic esophagitis (EE). [1] We bring this to your attention because interns and junior residents rotating through the emergency department (ED) and intensive care have little experience with food impactions and the accompanying differential diagnoses, and their inexperience may lead to a delay in diagnosis and/or treatment.
Single training sample Face recognition using fusion of Gabor responses

This paper deals with Single training sample Face recognition which is a new challenging problem in pattern recognition and machine vision. In the proposed model, Gabor filter is applied on face images, to generate four Gabor responses. And then, the generated samples along with the original image used as the input of five Nearest Neighbor Base-classifiers. To increase the correct recognition rate, the votes of Base-Classifiers are combined using majority voting technique. The correct class of each test sample is determined by the majority of the classifiers votes. But in cases which the winner class can't be determined using majority voting (deep uncertainty), we use Enhanced Majority voting which chooses the vote of original image's Base-Classifier as the winner class. The resultant recognition rate of applying this model on ORL face database was improvement in recognition rate about 2%, 4% and 5% than 2DPCA, (PC)2 A and PCA respectively.
Supporting Orthographic Learning at the Beginning Stage of Learning to Read Chinese as a Second Language

Learning to read a second language (L2) is especially challenging when a target L2 requires learning new graphic forms. Learning Chinese, which consists of thousands of characters composed of hundreds of basic writing units, presents such a challenge of orthographic learning for adult English speakers at the beginning stages of learning. In this study, we use an in vivo classroom design to extend previous research on how to support orthographic learning. First, we test the hypothesis that learning characters is enhanced by a grouped sequence of characters that share sub-character graphic components. Second, we examine the effects of four encoding methods that have been investigated in laboratory studies—handwriting, visual chunking, passive reading, and stroke-reporting. The results demonstrate that the grouped approach facilitated character production compared with the distributed approach and that visual-chunking outperformed the other three encoding methods under the grouped sequence. We propose that learning via visual chunking with characters grouped by the same chunks enhances the Chinese orthographic representations of beginning L2 learners.