Miracle-dz/UniFAR-FTUs huggingface dataset:
Chlamydia trachomatis contains a protein similar to the Legionella pneumophila mip gene product

A 27kDa Chlamydia trachomatis L2 protein was characterized by the use of monoclonal antibodies and by two‐dimensional gel electrophoresis. The protein was shown to be located in the membrane of reticulate bodies as well as elementary bodies. Its synthesis could be detected from 10 hours post‐infection. Cloning and sequence analysis of the distal part of the gene revealed an open reading frame of 175 amino acids. Comparison of the deduced amino acid sequence with the NBRF data base revealed significant homology between the 27kDa chlamydial membrane protein and the product of the macrophage infectivity potentiator (mip) gene of Legionella pneumophila.
Ragnarok : RAndom Graphs Never ARe OK

Many researchers test graph scheduling algorithms on “random” graphs. We show that many of the random graphs used in the literature are not representative of actual programs by comparing random graphs to graphs derived from the SPECINT2000 benchmarks. We introduce Ragnarok (RAndom Graphs Never ARe OK), a new graph benchmark suite embodying characteristics of SPECINT2000 programs. We hope this benchmark suite will be used instead of random graphs.
Framing the experience of residence abroad: The pedagogical function of the informal interview

The informal, in‐depth interview is a frequently used tool in qualitative research, where the main purpose is to gain an understanding for the interviewer of (part of) the world‐view of the interviewee. The argument in this article is that the interview process itself helps the interviewee to develop a new understanding of the experiences which are in focus. The interview has a pedagogical function for the interviewee which is dependent upon the interaction with the interviewer. This argument is illustrated from interviews with primary school teachers in France who spend a year living and working in Portugal. They develop, in and through the interview, a set of more or less closely defined concepts which help them to understand this experience. The article ends with a proposal that this function of the interview should be introduced into in‐service training involving a stay abroad and an encounter with otherness.
THE APPLICATION OF TWO FREE‐CHOICE PROFILE METHODS TO INVESTIGATE THE SENSORY CHARACTERISTICS OF CHOCOLATE

The concept of free-choice profiling allows untrained assessors to participate in sensory profiling. However, it is sometimes the case that such individuals are unable to describe what they perceive when the samples are presented in the isolation of the sensory testing booths. This paper reports an experiment to compare the usual free-choice profile procedure, with a more structured approach based on Kelly's repertory grid method. Generalized Procrustes analysis was used to analyse the data. The sample configurations obtained from both approaches were very similar, as were the interpretations of the main perceptual dimensions.
Pancreatic Ductal Adenocarcinoma Encapsulated by a Tumor-Forming Type 1 Autoimmune Pancreatitis Located at the Pancreatic Tail: A Case Report

Abstract Introduction Autoimmune pancreatitis (AIP) is recognized as a disease with a good prognosis that responds well to steroids, but the complication of pancreatic ductal adenocarcinoma (PDAC) in AIP is a rare condition. We report a case of PDAC encapsulated by tumor-forming type 1 AIP. Case Presentation The patient, a 65-year-old female, was found to have high CA19-9 levels and a pancreatic mass with a diameter of 30 mm on abdominal ultrasonography. Contrast-enhanced computed tomography revealed a 40-mm mass in the tail of the pancreas that had a 27-mm oligemic mass inside it. From these work-up examinations, this tumor was diagnosed as PDAC, with evidence of colonic invasion. As curative resection for PDAC, a distal pancreatectomy with splenectomy and combined colon resection were performed. Histopathological examination showed invasive PDAC surrounded by IgG4-positive plasma cell infiltration. Based on these findings, a diagnosis was made of PDAC located in the pancreatic tail capsulized by type 1 AIP. The postoperative course was uneventful, and the patient was discharged on postoperative day 15. She underwent postoperative adjuvant chemotherapy with S-1 for 6 months, and no recurrence was noted for 2 years after operation. Conclusion Currently, there are two hypothetical mechanisms of PDAC induction by AIP: (1) carcinogenic stimulation due to chronic inflammation and (2) paraneoplastic syndrome caused by AIP. Further study of the relationship between AIP and pancreatic cancer is needed, and follow-up should be conducted while keeping in mind the possibility of complications.
Sizing and placement of charge recycling transistors in MTCMOS circuits

A downside of using Multi-Threshold CMOS (MTCMOS) technique for leakage reduction is the energy consumption during transitions between sleep and active modes. Previously, a charge recycling (CR) MTCMOS architecture was proposed to reduce the large amount of energy consumption that occurs during the mode transitions in power-gated circuits. Considering the RC parasitics of the virtual ground and VDD lines, proper sizing and placement of charge-recycling transistors is key to achieving the maximum power saving. In this paper, we show that the sizing and placement problems of charge-recycling transistors in CR-MTCMOS can be formulated as a linear programming problem, and hence, can be efficiently solved using standard mathematical programming packages. The proposed sizing and placement techniques allow us to employ the CR-MTCMOS solution in large row-based standard cell layouts while achieving nearly the full potential of this power-gating architecture, i.e., we achieve 44% saving in switching energy due to the mode transition in CR-MTCMOS compared to standard MTCMOS.
Family conflict and child adjustment: Evidence for a cognitive-contextual model of intergenerational transmission.

Three cohorts of 10-to 14-year-old adolescents were sampled to obtain perceptions of their parents' conflict-resolution styles, their own conflict-resolution styles, and their behavioral adjustment, to test J. H. Grych and F. D. Fincham's (1990) cognitive-contextual model of the relationship of marital conflict to child adjustment. As found previously, boys and girls were not exposed to different levels or types of interparental conflict, although boys tended to blame themselves more. Adolescents' reports of their own conflict-resolution styles with siblings were clearly related to level and types of their more general adjustment levels. A series of regressions supported Grych and Fincham's model for internalizing problems (and avoidant resolution style) in adolescents; only minimal support was found with externalizing problems (and attacking resolution style). Gender-specific patterns of intergenerational transmission of resolution styles were found and are discussed.
No replication of direct neuronal activity–related (DIANA) fMRI in anesthetized mice

Direct imaging of neuronal activity (DIANA) by functional magnetic resonance imaging (fMRI) could be a revolutionary approach for advancing systems neuroscience research. To independently replicate this observation, we performed fMRI experiments in anesthetized mice. The blood oxygenation level–dependent (BOLD) response to whisker stimulation was reliably detected in the primary barrel cortex before and after DIANA experiments; however, no DIANA–like fMRI peak was observed in individual animals’ data with the 50 to 300 trials. Extensively averaged data involving 1050 trials in six mice showed a flat baseline and no detectable neuronal activity–like fMRI peak. However, spurious, nonreplicable peaks were found when using a small number of trials, and artifactual peaks were detected when some outlier-like trials were excluded. Further, no detectable DIANA peak was observed in the BOLD-responding thalamus from the selected trials with the neuronal activity–like reference function in the barrel cortex. Thus, we were unable to replicate the previously reported results without data preselection.
Conformation-dependent QSAR approach for the prediction of inhibitory activity of bromodomain modulators

Abstract Epigenetic drug discovery is a promising research field with growing interest in the scientific community, as evidenced by the number of publications and the large amount of structure-epigenetic activity information currently available in the public domain. Computational methods are valuable tools to analyse and understand the activity of large compound collections from their structural information. In this manuscript, QSAR models to predict the inhibitory activity of a diverse and heterogeneous set of 88 organic molecules against the bromodomains BRD2, BRD3 and BRD4 are presented. A conformation-dependent representation of the chemical structures was established using the RDKit software and a training and test set division was performed. Several two-linear and three-linear QuBiLS-MIDAS molecular descriptors (www.tomocomd.com) were computed to extract the geometric structural features of the compounds studied. QuBiLS-MIDAS-based features sets, to be used in the modelling, were selected using dimensionality reduction strategies. The multiple linear regression procedure coupled with a genetic algorithm were employed to build the predictive models. Regression models containing between 6 to 9 variables were developed and assessed according to several internal and external validation methods. Analyses of outlier compounds and the applicability domain for each model were performed. As a result, the models against BRD2 and BRD3 with 8 variables and the model with 9 variables against BRD4 were those with the best overall performance according to the criteria accounted for. The results obtained suggest that the models proposed will be a good tool for studying the inhibitory activities of drug candidates against the bromodomains considered during epigenetic drug discovery.
Dyslexia: Questions from a Social Psychological Perspective

Summary This article suggests that the definition and identification of dyslexia/specific learning difficulties from the paradigm of cognitive psychology may be helpfully complemented by a greater appeal to a social psychology perspective. In particular, in drawing upon this perspective, questions are raised which might provide a positive way forward for educational psychologists (EPs) and others with an interest in dyslexia.
Identification and Detection of Prokaryotic Symbionts in the Ciliate Metopus from Anaerobic Granular Sludge

The aim of the present study was to investigate the prokaryotic community structure of the anaerobic ciliate, Metopus sp. using rRNA sequencing, fluorescence in situ hybridization (FISH), and transmission electron microscopy (TEM). Metopus sp. was physically separated from anaerobic granular sludge in a domestic wastewater treatment plant and anoxically cultivated for 7 d. 16S rRNA gene sequences from the prokaryotes Methanoregula boonei and Clostridium aminobutyricum were abundantly detected in Metopus ciliates. The FISH analysis using the oligonucleotide probes Mg1200b and Cla568 demonstrated that these prokaryotes were localized within Metopus cells. These results identify M. boonei- and C. aminobutyricum-like prokaryotes as novel endosymbionts of Metopus ciliates.
Human Core Temperature Responses during Exercise and Subsequent Recovery: An Important Interaction between Diurnal Variation and Measurement Site

Chronobiological investigations into core temperature during and after exercise can involve ambulatory measurements of intestinal temperature during actual competitions, esophageal temperature measurements in laboratory simulations, or rectal temperature, which can be measured in both the field and laboratory. These sites have yet to be compared during both morning and afternoon exercise and subsequent recovery. At 08∶00 and 17∶00 h, seven recreationally active males exercised at 70% peak oxygen uptake for 30 min and then recovered passively for 30 min. During the experiment, esophageal, rectal, intestinal, and skin temperatures, plus sweat loss, heart rate, and ratings of perceived exertion (RPE), were monitored. We found that the diurnal variation in intestinal temperature responses (0.45±0.32°C; mean±SD) was significantly larger compared with rectal (0.33±0.24°C) and, particularly, esophageal temperature responses (0.21±0.20°C; p= 0.019). This reflected a greater difference of 0.25–0.40°C between the esophagus and the other two sites in the afternoon, compared to inter‐site differences of only 0.13–0.16°C in the morning. Diurnal variation was small for skin temperature, heart rate, sweat loss, and RPE responses during exercise (p>0.05). Our data suggest that the relative differences between intestinal, rectal, and esophageal temperature during exercise and subsequent recovery depend on time of day to the extent that inferences from studies on experimental and applied chronobiology will be affected.
YABBY Polarity Genes Mediate the Repression of KNOX Homeobox Genes in Arabidopsis

The YABBY (YAB) genes specify abaxial cell fate in lateral organs in Arabidopsis. Loss-of-function mutants in two early-expressing YAB genes, FILAMENTOUS FLOWER (FIL) and YAB3, do not exhibit vegetative phenotypes as a result of redundancy. Mutations in these genes result in the derepression of the KNOX homeobox genes SHOOTMERISTEMLESS (STM), BREVIPEDICELLUS, and KNAT2 in the leaves and in the partial rescue of stm mutants. Here, we show that fil yab3 double mutants exhibit ectopic meristem formation on the adaxial surfaces of cotyledons and leaf blades. We propose that in addition to abaxial specification, lateral organ development requires YAB function to downregulate KNOTTED homeobox genes so that meristem initiation and growth are restricted to the apex.
Therapeutic human papillomavirus DNA vaccination strategies to control cervical cancer

A persistent human papillomavirus (HPV) infection is considered causal and necessary for the continued growth of cervical cancer. Thus, vaccination against HPV represents a plausible approach to prevent and treat cervical cancer. A report in the current issue of the European Journal of Immunology describes a therapeutic HPV DNA vaccination strategy using the HPV‐16 E7 antigen fused to the invariant chain to enhance the E7‐specific CD8+ and CD4+ T cell immune responses, resulting in a potent anti‐tumor effect against E7‐expressing tumors. Continued exploration of HPV therapeutic DNA vaccines may lead to eventual clinical application.
Discrimination and Sleep

Ethnic minority adolescents experience certain sleep problems, yet factors that affect their sleep are poorly understood. This study examined the association between ethnic discrimination and sleep during adolescence and the extent to which perceived stress mediated these associations. This study also examined whether school belonging can protect adolescents from discrimination’s negative association with sleep. Latino (n = 247) and Asian American (n = 113) adolescents (Mage=17.18, SD = .75; 57% female) completed self-reports of overt and subtle discrimination, sleep quality, sleep hours, perceived stress, and school belonging. Both overt and subtle discrimination were associated with worse sleep quality. Only subtle discrimination was associated with getting less sleep. The associations between discrimination and sleep hold even after controlling for perceived stress. School belonging buffered the negative effect of overt discrimination on sleep. Findings suggest that discrimination is a unique type of vigilance that affects sleep; however, school belonging may be a positive resource for adolescents.
On lightcone string field theory from Super Yang-Mills and holography

We investigate the issues of holography and string interactions in the duality between SYM and the pp wave background. We argue that the Penrose diagram of the maximally supersymmetric pp-wave has a one dimensional boundary. This fact suggests that the holographic dual of the pp-wave can be described by a quantum mechanical system. We believe this quantum mechanical system should be formulated as a matrix model. From the SYM point of view this matrix model is built out of the lowest lying KK modes of the SYM theory on an $S^3$ compactification, and it relates to a wave which has been compactified along one of the null directions. String interactions are defined by finite time amplitudes on this matrix model. For closed strings they arise as in AdS-CFT, by free SYM diagrams. For open strings, they arise from the diagonalization of the hamiltonian to first order in perturbation theory. Estimates of the leading behaviour of amplitudes in SYM and string theory agree, although they are performed in very different regimes. Corrections are organized in powers of $1/(\mu \alpha ' p^+)^2$ and $g^2(\mu \alpha ' p^+)^4$.
Motion Editing with Prioritized Constraints

We propose an intuitive motion editing technique allowing the end-user to transform an original motion by applying position constraints on freely selected locations of the character body. The major innovation comes from the possibility to assign a priority level to each constraint. The resulting scale of user-defined priority levels allows to handle multiple asynchronously overlapping constraints. As a consequence the end user can enforce a larger range of natural behaviors where conflicting constraints compete to control a common set of joints. By default the joint angles of the original motion are preserved as the lowest priority constraint. However, in case a Cartesian constraint from the original motion is essential, it is straightforward to define a high priority constraint that will retain it before enforcing other lower priority constraints. Additional features are proposed to provide a more productive motion editing process like defining the constraints relative to a mobile frame and precisely specifying which joints are recruited by each constrain. The current limitation remains its computing cost which will be improved in future work.
Ethnographic performance and its flexibility in researching a traditional healing system in southern Thailand

Purpose – The purpose of this paper is to discuss the experience of carrying out an ethnographic research in the real world with six different participant groups from different backgrounds and embodying different expertise in traditional medicine. The paper will discuss why some approaches do not go well with some key informant groups and will demonstrate a suitable method that function better with those groups. The paper also argues that there is unpredictability of doing research in the real world, and this is crucial knowledge for novice researchers, and researchers who wish to embark on their research in different communities. Design/methodology/approach – Ethnography comprising of in-depth interviews, participant observation, focus group and unobtrusive methods. Findings – Listening to traditional healers’ explanation of their roles, patients’ perspectives of their treatments and the views of other participant groups will help us to understand the role of traditional healers, how effective their trea.
Illusory conjunctions in French: The nature of sublexical units in visual word recognition

The respective influence of orthographic redundancy (Seidenberg, 1987) and syllable boundaries (Rapp, 1992) on reading units in French was tested in three experiments, using the illusory conjunction paradigm (Prinzmetal, Treiman, & Rho, 1986). Bigram boundaries were defined according to bigram frequencies. The data showed that the syllable effect was attenuated or cancelled when syllable boundaries did not coincide with bigram boundaries. Reading units were defined by syllable and orthographic information. The implications of such findings for the dual route theory and the PDP model are discussed.
The effect of biocompatible peritoneal dialysis solutions on neutrophil to lymphocyte ratio

Abstract Introduction: Long-term exposure to dialysis solutions is an important contributor to the ongoing inflammatory process in peritoneal dialysis (PD) patients. Some studies have shown amelioration of this adverse effect with biocompatible solutions. We aimed to compare the neutrophil-to-lymphocyte (N/L) ratio in PD patients using biocompatible and standard solutions and to find out the association between N/L ratio and peritonitis indices. Materials and methods: This was a cross-sectional, multicenter study involving 120 prevalent PD patients. Seventy-one patients (59%) were using biocompatible solutions and 49 patients (41%) were using standard solutions. From blood samples, N/L ratio and platelet-to-lymphocyte ratio were calculated and mean platelet volume, erythrocyte sedimentation rate and hs-CRP values were detected. Data regarding the peritonitis rate and time to first peritonitis episode were also recorded. Results: Biocompatible and standard groups were similar regarding age and gender. N/L ratio and hs-CRP levels have been found significantly higher in patients using biocompatible solutions (3.75 ± 1.50 vs. 3.27 ± 1.3, p = 0.04 and 3.2 ± 2.5 vs. 1.8 ± 2.0, p < 0.01, respectively). Peritonitis rates and time to the first peritonitis episode were found similar in patients using both types of solutions (0.23 ± 0.35 vs. 0.27 ± 0.32, p = 0.36 and 32.8 ± 35.8 vs. 21.5 ± 26.9 months, p = 0.16, respectively). Discussion: N/L ratio was significantly higher in biocompatible solution users in parallel to hs-CRP levels, so biocompatible solutions seem to be related with increased inflammation in PD patients. Although we cannot make a certain explanation, we assume that there may be an association between acidity of the peritoneal content and virulence of microorganisms.
A Survey on Methods and Models of Eye Tracking, Head Pose and Gaze Estimation

Eye tracking and Gaze estimation are the most challenging areas in computer vision. Even though we have achieved a significant progress in the last few decades, some domains are still facing the limitations. Be it the lack of accuracy due to the design of fovea or the tracking challenges in visible spectrum, this paper covers an in-depth research survey of the recent as well as the archaic methods and models used for eye tracking, head pose and gaze estimation. Index Terms – Eye detection and tracking, methods and models of eye tracking, head pose and gaze estimation, research survey paper, visible spectrum.
Real Time Metagenomics: Using k-mers to annotate metagenomes

Summary: Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community. Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at http://edwards.sdsu. edu/rtmg. In addition, code to access the annotation servers is available for download from http://www.theseed. org/. FIGfams and k-mers are available for download from ftp://ftp.theseed. org/FIGfams/. Contact: redwards@mail.sdsu. edu Supplementary information: Supplementary data are available at Bioinformatics online.