Miracle-dz/UniFAR-FTUs huggingface dataset:
More Than Meets the Eye: Associations of Vaginal Bacteria with Gram Stain Morphotypes Using Molecular Phylogenetic Analysis

Bacterial vaginosis (BV) is a highly prevalent condition associated with adverse health outcomes. Gram stain analysis of vaginal fluid is the standard for confirming the diagnosis of BV, wherein abundances of key bacterial morphotypes are assessed. These Lactobacillus, Gardnerella, Bacteroides, and Mobiluncus morphotypes were originally linked to particular bacterial species through cultivation studies, but no studies have systematically investigated associations between uncultivated bacteria detected by molecular methods and Gram stain findings. In this study, 16S-rRNA PCR/pyrosequencing was used to examine associations between vaginal bacteria and bacterial morphotypes in 220 women with and without BV. Species-specific quantitative PCR (qPCR) and fluorescence in Situ hybridization (FISH) methods were used to document concentrations of two bacteria with curved rod morphologies: Mobiluncus and the fastidious BV-associated bacterium-1 (BVAB1). Rank abundance of vaginal bacteria in samples with evidence of curved gram-negative rods showed that BVAB1 was dominant (26.1%), while Mobiluncus was rare (0.2% of sequence reads). BVAB1 sequence reads were associated with Mobiluncus morphotypes (p<0.001). Among women with curved rods, mean concentration of BVAB1 DNA was 2 log units greater than Mobiluncus (p<0.001) using species-specific quantitative PCR. FISH analyses revealed that mean number of BVAB1 cells was 2 log units greater than Mobiluncus cells in women with highest Nugent score (p<0.001). Prevotella and Porphyromonas spp. were significantly associated with the “Bacteroides morphotype,” whereas Bacteroides species were rare. Gram-negative rods designated Mobiluncus morphotypes on Gram stain are more likely BVAB1. These findings provide a clearer picture of the bacteria associated with morphotypes on vaginal Gram stain.
Heart rate variability from 24-hour electrocardiography and the 2-year risk for sudden death.

BACKGROUND Low heart rate variability has been implicated as a risk factor for sudden death. However, no large epidemiological studies using sudden death as an outcome event have been reported. METHODS AND RESULTS A total of 6,693 consecutive patients who underwent 24-hour ambulatory ECG were followed up for 2 years; of these, 245 patients died suddenly. Clinical data at the time of 24-hour ambulatory ECG were collected for all patients who died suddenly and for a random sample of 268 patients from the study cohort. In all patients in sinus rhythm with or without occasional supraventricular arrhythmias at the 24-hour ECG (193 patients who died suddenly and 230 patients from the sample), heart rate variability parameters were derived. Patients with low short-term RR interval variability (mean during 24 hours of per-minute standard deviations [SD] of RR intervals < 25 msec) had a 4.1-fold higher risk (95% confidence interval [CI], 2.6, 8.1) for sudden death than patients with high short-term variability (> or = 40 msec); after adjustment for age, evidence of cardiac dysfunction, and history of myocardial infarction, the relative risk was 2.6 (95% CI, 1.4, 5.1). The crude relative risk of long-term RR interval variability (SD during 24 hours of per-minute means of RR intervals < 8 msec) was 4.4 (95% CI, 2.6, 7.7); after adjustment for the same risk factors, it was 2.2 (95% CI, 1.2, 4.1). Patients with a minimum heart rate > or = 65 beats per minute had a double risk of sudden death compared with those with a minimum heart rate < 65 beats per minute (adjusted relative risk, 2.1; 95% CI, 1.3, 3.6). CONCLUSIONS These findings support the theory that patients with low parasympathetic activity (low short-term RR interval variability) have an increased risk for sudden death independent of other risk factors.
Computer-Mediated Communication and Gender Difference: A Meta-Analysis

The purpose of this review paper is to conduct an extensive meta-analysis of the empirical literature on gender difference in the use of computer-mediated communication (CMC). Specifically, the questions that this research addresses are: 1) Are there gender differences in people’s behaviors in relation to CMC? If yes, to what extent? 2) What study features moderate the gender effects on the outcomes in a CMC environment? In this paper, 321 independent effect sizes were extracted from 50 studies involving a total of 63889 users exploring the gender difference in the use of CMC. The results of this study show that just like in face-to-face environments, gender related stereotypical patterns do exist in virtual environments.
Daple is a novel non-receptor GEF required for trimeric G protein activation in Wnt signaling

Wnt signaling is essential for tissue homeostasis and its dysregulation causes cancer. Wnt ligands trigger signaling by activating Frizzled receptors (FZDRs), which belong to the G-protein coupled receptor superfamily. However, the mechanisms of G protein activation in Wnt signaling remain controversial. In this study, we demonstrate that FZDRs activate G proteins and trigger non-canonical Wnt signaling via the Dishevelled-binding protein, Daple. Daple contains a Gα-binding and activating (GBA) motif, which activates Gαi proteins and an adjacent domain that directly binds FZDRs, thereby linking Wnt stimulation to G protein activation. This triggers non-canonical Wnt responses, that is, suppresses the β-catenin/TCF/LEF pathway and tumorigenesis, but enhances PI3K-Akt and Rac1 signals and tumor cell invasiveness. In colorectal cancers, Daple is suppressed during adenoma-to-carcinoma transformation and expressed later in metastasized tumor cells. Thus, Daple activates Gαi and enhances non-canonical Wnt signaling by FZDRs, and its dysregulation can impact both tumor initiation and progression to metastasis. DOI: http://dx.doi. org/10.7554/eLife.07091. 001
Healthy Cats Are Commonly Colonized with “Helicobacter heilmannii” That Is Associated with Minimal Gastritis

ABSTRACT Gastric Helicobacter infection in healthy pet cats is not well characterized. We performed endoscopy with gastric biopsy on 15 healthy pet cats that were rigorously screened to exclude underlying or concurrent diseases that might affect Helicobactercolonization. Gastric mucosa biopsy specimens were examined by histology, culture, and PCR for the presence ofHelicobacter infection and by histology for the presence of gastritis. Of 15 cats, all but 1 had gastricHelicobacter-like organisms (GHLOs) on examination by light microscopy, and in the one histologically negative cat, GHLOs were detected by PCR. Gastric inflammation was mild or was absent for all cats. No Helicobacter species were identified by culture. Analysis of the 16S rRNA sequence from Helicobacter strains from 10 cats showed that all bacteria were closely related toHelicobacter felis, although there was heterogeneity among the sequences. These results suggest that the gastric mucosa of healthy pet cats is commonly colonized with an uncultivatedHelicobacter that is closely related to H. felis, is associated with little or no gastritis, and shows heterogeneity in its 16S rRNA sequence. The epithet “Helicobacter heilmannii” continues to be an appropriate working designation for these bacteria.
B cell antigen receptor signal strength and peripheral B cell development are regulated by a 9-O-acetyl sialic acid esterase

We show that the enzymatic acetylation and deacetylation of a cell surface carbohydrate controls B cell development, signaling, and immunological tolerance. Mice with a mutation in sialate:O-acetyl esterase, an enzyme that specifically removes acetyl moieties from the 9-OH position of α2–6-linked sialic acid, exhibit enhanced B cell receptor (BCR) activation, defects in peripheral B cell development, and spontaneously develop antichromatin autoantibodies and glomerular immune complex deposits. The 9-O-acetylation state of sialic acid regulates the function of CD22, a Siglec that functions in vivo as an inhibitor of BCR signaling. These results describe a novel catalytic regulator of B cell signaling and underscore the crucial role of inhibitory signaling in the maintenance of immunological tolerance in the B lineage.
A laboratory exercise for visible gel filtration chromatography using fluorescent proteins

Gel filtration chromatography (GFC) separates molecules according to size and is one of the most widely used methods for protein purification. Here, red fluorescent protein (RFP), green fluorescent protein (GFP), yellow fluorescent protein (YFP), cyan fluorescent protein (CFP), and/or their fusion proteins were prokaryotically expressed, purified, and used in a laboratory exercise to intuitively demonstrate GFC. Different bands, corresponding to RFP, RFP‐CFP (RC), YFP‐RFP‐YFP (YRY), and pyruvate kinase II‐GFP (PKG) were well separated on a Superdex 200 column from a 0.5‐mL sample. Increasing the sample volume and changing the chromatographic resin to Sephadex G‐100 resulted in lower resolution separation. Students enjoyed identifying combinations of colored proteins and found this exercise helpful for understanding the factors that affect GFC resolution. © 2014 by The International Union of Biochemistry and Molecular Biology, 43(1):33–38, 2015.
Distributed Coordination and Data Fusion for Multi-robot Search

This paper presents coordination and data fusion methods for teams of vehicles performing target search task s without guaranteed communication. A fully distributed team planning algorithm is proposed that utilizes limited shared information as it becomes available, and data fusion techni ques are introduced for merging estimates of the target’s positi on from vehicles that regain contact after long periods of time. The proposed data fusion techniques are shown to avoid overcounting information, which ensures that combining data from different vehicles will not decrease the performance of the search. Motivated by the underwater search domain, a realis tic underwater acoustic communication channel is used to deter mine the probability of successful data transfer between two loc ations. The channel model is validated using acoustic communicatio n data and integrated into a simulation of multiple autonomous vehicles in both open ocean and harbor environments. The results demonstrate that distributed coordination with limited communication significantly improves team performance ver sus prior techniques that continually maintain connectivity.
The Role of Gender on Communication Strategy Use.

A study investigated: (1) the communication strategies (CSs) used by Turkish learners of English as a Second Language (ESL) when interacting with native English speakers, and (2) the influence of gender on use of CSs when communication difficulties occur because of limited English proficiency. Subjects were ten native Turkish-speaking ESL learners paired with ten native English speakers. Conversations were recorded and transcribed, and CSs were coded. Analysis indicates the CSs used by the ESL learners included reduction strategies, generalization, paraphrase, word coinage, cooperative strategies, repair, and repetition. Results also revealed that gender of the native English speaker had an important effect on use of CSs in both sameand opposite-sex dyads; all Turkish ESL learners used more CSs with female than with male interlocutors. It is concluded that communication success depends on pairing, particularly in native-nonnative interaction where cooperation is required, and on interlocutors' personalities. Implications concerning the teaching of CSs are examined. Contains 20 references. (MSE) ******************************************************************************** Reproductions supplied by EDRS are the best that can be made from the original document. ******************************************************************************** THE ROLE OF GENDER ON COMMUNICATION STRATEGY USE by Zeynep Kogo4lu
Evaluating pharmacological models of high and low anxiety in sheep

New tests of animal affect and welfare require validation in subjects experiencing putatively different states. Pharmacological manipulations of affective state are advantageous because they can be administered in a standardised fashion, and the duration of their action can be established and tailored to suit the length of a particular test. To this end, the current study aimed to evaluate a pharmacological model of high and low anxiety in an important agricultural and laboratory species, the sheep. Thirty-five 8-month-old female sheep received either an intramuscular injection of the putatively anxiogenic drug 1-(m-chlorophenyl)piperazine (mCPP; 1 mg/kg; n = 12), an intravenous injection of the putatively anxiolytic drug diazepam (0.1 mg/kg; n = 12), or acted as a control (saline intramuscular injection n = 11). Thirty minutes after the treatments, sheep were individually exposed to a variety of tests assessing their general movement, performance in a ‘runway task’ (moving down a raceway for a food reward), response to startle, and behaviour in isolation. A test to assess feeding motivation was performed 2 days later following administration of the drugs to the same animals in the same manner. The mCPP sheep had poorer performance in the two runway tasks (6.8 and 7.7 × slower respectively than control group; p < 0.001), a greater startle response (1.4 vs. 0.6; p = 0.02), a higher level of movement during isolation (9.1 steps vs. 5.4; p < 0.001), and a lower feeding motivation (1.8 × slower; p < 0.001) than the control group, all of which act as indicators of anxiety. These results show that mCPP is an effective pharmacological model of high anxiety in sheep. Comparatively, the sheep treated with diazepam did not display any differences compared to the control sheep. Thus we suggest that mCPP is an effective treatment to validate future tests aimed at assessing anxiety in sheep, and that future studies should include other subtle indicators of positive affective states, as well as dosage studies, so conclusions on the efficacy of diazepam as a model of low anxiety can be drawn.
Observing Motorway Driving Violations

Why is it important to study driving violations? Observational data from over 20 years ago established that close following and other violations are statistically related to drivers’ crash involvement (Evans & Wasielewski, 1982; 1983). From questionnaire studies, Parker, Reason, Manstead, and Stradling (1995) report that driving violations are statistically associated with crash involvement. Golias and Karlaftis (2002) found that while speeding was associated with dangerous driving violations, neither was related to non-seat belt use or drink-driving violations. Kontogiannis, Kossiavelou, and Marmaras (2002) found that highway-code violations were related to speeding convictions. From telephone survey data, Jonah (1990) found that younger drivers reported higher accident and violation rates – including speeding and tailgating. Studies in several countries have found that males and younger drivers report significantly more violations than do females and older drivers (e.g., Kontogiannis et al., 2002; Lawton, Parker, & Stradling, 1997; Mesken, Lajunen, & Summala, 2002). Greater understanding of driving violations could serve to improve counter measures. From survey data of drivers’ reactions to speed camera installation, Corbett (2000) identified four driver types – “Conformers”, “Deterred” (reduced speed to avoid detection), “Manipulators” (slowed down only when approaching a speed camera), and “Defiers” (undeterred by speed cameras). Although percentages of Manipulators and Defiers were relatively small, they were important categories of violating drivers. Two questions are pertinent. Would observational data on a range of driver violating behaviors produce similar findings? Would analysis of such data emerge with a similar driver typology?
Multiple Fundamental Frequency Estimation and Polyphony Inference of Polyphonic Music Signals

This paper presents a frame-based system for estimating multiple fundamental frequencies (F0s) of polyphonic music signals based on the short-time Fourier transform (STFT) representation. To estimate the number of sources along with their F0s, it is proposed to estimate the noise level beforehand and then jointly evaluate all the possible combinations among pre-selected F0 candidates. Given a set of F0 hypotheses, their hypothetical partial sequences are derived, taking into account where partial overlap may occur. A score function is used to select the plausible sets of F0 hypotheses. To infer the best combination, hypothetical sources are progressively combined and iteratively verified. A hypothetical source is considered valid if it either explains more energy than the noise, or improves significantly the envelope smoothness once the overlapping partials are treated. The proposed system has been submitted to Music Information Retrieval Evaluation eXchange (MIREX) 2007 and 2008 contests where the accuracy has been evaluated with respect to the number of sources inferred and the precision of the F0s estimated. The encouraging results demonstrate its competitive performance among the state-of-the-art methods.
Wave-echo position control of flexible systems: towards an explanation and theory

An elegant, novel solution has been developed to the general problem of point-to-point control by a single actuator of a remote load through an intermediate flexible system. It is based on mechanical wave concepts. Under wide-ranging conditions it allows almost "perfect", vibrationless motion of the load. It requires minimal knowledge of the system dynamics and is robust to changes in load, to non-ideal actuator behaviour and to sensing errors. Transit times are excellent. In the start-up the system itself reveals to the controller how to terminate the motion, so that the real system acts as the controller model. In developing the strategy practice has preceded theory. This work presents and explores theoretical explanations of the success of the method.
A Noise Robust Multilingual Reference Recogniser Based on Speechdat(II)

An important aspect of noise robustness of automatic speech recognisers (ASR) is the proper handling of non-speech acoustic events. The present paper describes further improvements of an already existing reference recogniser towards achieving such kind of robustness. The reference recogniser applied is the COST 249 SpeechDat reference recogniser, which is a fully automatic, language-independent training procedure for building a phonetic recogniser (http://www.telenor.no/fou/prosjekter/taletek/refrec). The reference recogniser relies on the HTK toolkit and a Speech- Dat(II) compatible database, and is designed to serve as a reference system in multilingual speech recognition research. The paper describes version 0.96 of the reference recogniser which take into account labelled non-speech acoustic events during training and provides robustness against these during testing. Results are presented on small and medium vocabulary recognition for six languages.
Multiple Loci Modulate Opioid Therapy Response for Cancer Pain

Purpose: Patients treated with opioid drugs for cancer pain experience different relief responses, raising the possibility that genetic factors play a role in opioid therapy outcome. In this study, we tested the hypothesis that genetic variations may control individual response to opioid drugs in cancer patients. Experimental Design: We tested 1 million single-nucleotide polymorphisms (SNP) in European cancer patients, selected in a first series, for extremely poor (pain relief ≤40%; n = 145) or good (pain relief ≥90%; n = 293) responses to opioid therapy using a DNA-pooling approach. Candidate SNPs identified by SNP-array were genotyped in individual samples constituting DNA pools as well as in a second series of 570 patients. Results: Association analysis in 1,008 cancer patients identified eight SNPs significantly associated with pain relief at a statistical threshold of P < 1.0 × 10−3, with rs12948783, upstream of the RHBDF2 gene, showing the best statistical association (P = 8.1 × 10−9). Functional annotation analysis of SNP-tagged genes suggested the involvement of genes acting on processes of the neurologic system. Conclusion: Our results indicate that the identified SNP panel can modulate the response of cancer patients to opioid therapy and may provide a new tool for personalized therapy of cancer pain. Clin Cancer Res; 17(13); 4581–7. ©2011 AACR.
Single-crystal silicon actuator arrays for micro manipulation tasks

Arrays of electrostatic MEMS actuators have been fabricated using a modified, multi-layer SCREAM (S_ingle-C_rystal R_eactive E_tching and M_etallization) process. The devices consist of released, torsionally suspended grids with high aspect ratio single-crystal silicon (SCS) tips. They can be used to generate a force field for the manipulation of small, flat objects. Calculations and experiments show that the actuator array is strong enough to move macroscopic parts. An individual actuator can generate a force of approximately 10 /spl mu/N and a displacement of 5 /spl mu/m. Monolithic arrays have been built reaching a size of up to 10 cm/sup 2/, with up to 15000 individual single-crystal silicon actuators on one chip. We investigate micro actuators for manipulation tasks, and discuss important issues and trade-offs in design, processing and fabrication. We describe manipulation experiments in which small, flat objects where lifted and moved. We conclude with an outlook on applications of programmable actuator arrays to more elaborate micro manipulation tasks and give an outline on how they can be used for transporting, positioning, sorting, and assembly of small parts.
High-Order Low-Noise Microwave Active Recursive Filters

In this article, we present a three-pole lownoise microwave active recursive filter obtained by a cascade association of three first-order recursive cells. To minimize the noise factor of the filter we study two topologies of first-order recursive filter. For each topology we determine the values of the optimal couplings and gain needed to obtain the minimum noise factor. We validate our study with simulated and measured results.
Functionality and Limitations of Current Workflow Management Systems

Work(cid:13)ow systems hold the promise of facilitating the everyday operation of many enterprises and work environments. As a result, many commercial work(cid:13)ow management systems have been developed. These systems, although useful, do not scale well, have limited fault-tolerance, and are in(cid:13)exible in terms of interoperating with other work(cid:13)ow systems. In this paper, we discuss the limitations of contemporary work(cid:13)ow management systems, and then elaborate on various directions for research and potential future extensions to the design and modeling of work(cid:13)ow management systems.
Drosophila fly straight by fixating objects in the face of expanding optic flow

SUMMARY Flies, like all animals that depend on vision to navigate through the world, must integrate the optic flow created by self-motion with the images generated by prominent features in their environment. Although much is known about the responses of Drosophila melanogaster to rotating flow fields, their reactions to the more complex patterns of motion that occur as they translate through the world are not well understood. In the present study we explore the interactions between two visual reflexes in Drosophila: object fixation and expansion avoidance. As a fly flies forward, it encounters an expanding visual flow field. However, recent results have demonstrated that Drosophila strongly turn away from patterns of expansion. Given the strength of this reflex, it is difficult to explain how flies make forward progress through a visual landscape. This paradox is partially resolved by the finding reported here that when undergoing flight directed towards a conspicuous object, Drosophila will tolerate a level of expansion that would otherwise induce avoidance. This navigation strategy allows flies to fly straight when orienting towards prominent visual features.