Miracle-dz/UniFAR-FTUs huggingface dataset:
Involvement of the flagellar assembly pathway in Vibrio alginolyticus adhesion under environmental stresses

Adhesion is an important virulence factor of Vibrio alginolyticus. This factor may be affected by environmental conditions; however, its molecular mechanism remains unclear. In our previous research, adhesion deficient strains were obtained by culturing V. alginolyticus under stresses including Cu, Pb, Hg, and low pH. With RNA-seq and bioinformatics analysis, we found that all of these stress treatments significantly affected the flagellar assembly pathway, which may play an important role in V. alginolyticus adhesion. Therefore, we hypothesized that the environmental stresses of the flagellar assembly pathway may be one way in which environmental conditions affect adhesion. To verify our hypothesis, a bioinformatics analysis, QPCR, RNAi, in vitro adhesion assay and motility assay were performed. Our results indicated that (1) the flagellar assembly pathway was sensitive to environmental stresses, (2) the flagellar assembly pathway played an important role in V. alginolyticus adhesion, and (3) motility is not the only way in which the flagellar assembly pathway affects adhesion.
Star Formation in AEGIS Field Galaxies since z = 1.1: The Dominance of Gradually Declining Star Formation, and the Main Sequence of Star-forming Galaxies

We analyze star formation (SF) as a function of stellar mass (M*) and redshift z in the All-Wavelength Extended Groth Strip International Survey. For 2905 field galaxies, complete to 1010(1010.8) M☉ at z < 0.7(1), with Keck spectroscopic redshifts out to z = 1.1, we compile SF rates (SFRs) from emission lines, GALEX, and Spitzer MIPS 24 μm photometry, optical-NIR M* measurements, and HST morphologies. Galaxies with reliable signs of SF form a distinct "main sequence" (MS), with a limited range of SFRs at a given M* and z (1 σ ≲ ±0.3 dex), and log(SFR) approximately proportional to log M*. The range of log(SFR) remains constant to z > 1, while the MS as a whole moves to higher SFR as z increases. The range of the SFR along the MS constrains the amplitude of episodic variations of SF and the effect of mergers on the SFR. Typical galaxies spend ~67%(95%) of their lifetime since z = 1 within a factor of ≲2(4) of their average SFR at a given M* and z. The dominant mode of the evolution of SF since z ~ 1 is apparently a gradual decline of the average SFR in most individual galaxies, not a decreasing frequency of starburst episodes, or a decreasing factor by which SFRs are enhanced in starbursts. LIRGs at z ~ 1 seem to mostly reflect the high SFR typical for massive galaxies at that epoch. The smooth MS may reflect that the same set of few physical processes governs SF prior to additional quenching processes. A gradual process like gas exhaustion may play a dominant role.
Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution

The cyanobacterial hsp17 ribonucleicacid thermometer (RNAT) is one of the smallest naturally occurring RNAT. It forms a single hairpin with an internal 1×3-bulge separating the start codon in stem I from the ribosome binding site (RBS) in stem II. We investigated the temperature-dependent regulation of hsp17 by mapping individual base-pair stabilities from solvent exchange nuclear magnetic resonance (NMR) spectroscopy. The wild-type RNAT was found to be stabilized by two critical CG base pairs (C14-G27 and C13-G28). Replacing the internal 1×3 bulge by a stable CG base pair in hsp17rep significantly increased the global stability and unfolding cooperativity as evidenced by circular dichroism spectroscopy. From the NMR analysis, remote stabilization and non-nearest neighbour effects exist at the base-pair level, in particular for nucleotide G28 (five nucleotides apart from the side of mutation). Individual base-pair stabilities are coupled to the stability of the entire thermometer within both the natural and the stabilized RNATs by enthalpy–entropy compensation presumably mediated by the hydration shell. At the melting point the Gibbs energies of the individual nucleobases are equalized suggesting a consecutive zipper-type unfolding mechanism of the RBS leading to a dimmer-like function of hsp17 and switch-like regulation behaviour of hsp17rep. The data show how minor changes in the nucleotide sequence not only offset the melting temperature but also alter the mode of temperature sensing. The cyanobacterial thermosensor demonstrates the remarkable adjustment of natural RNATs to execute precise temperature control.
Can Anopheles gambiae Be Infected with Wolbachia pipientis? Insights from an In Vitro System

ABSTRACT Wolbachia pipientis are maternally inherited endosymbionts associated with cytoplasmic incompatibility, a potential mechanism to drive transgenic traits into Anopheles populations for malaria control. W. pipientis infections are common in many mosquito genera but have never been observed in any Anopheles species, leading to the hypothesis that Anopheles mosquitoes are incapable of harboring infection. We used an in vitro system to evaluate the ability of Anopheles gambiae cells to harbor diverse W. pipientis infections. We successfully established W. pipientis infections (strains wRi and wAlbB) in the immunocompetent Anopheles gambiae cell line Sua5B. Infection was confirmed by PCR, antibiotic curing, DNA sequencing, and direct observation using fluorescence in situ hybridization. The infections were maintained at high passage rates for >30 passages. Our results indicate that there is no intrinsic genetic block to W. pipientis infection in A. gambiae cells, suggesting that establishment of in vivo W. pipientis infections in Anopheles mosquitoes may be feasible.
Dietary seed oil rich in conjugated linolenic acid from bitter melon inhibits azoxymethane‐induced rat colon carcinogenesis through elevation of colonic PPARγ expression and alteration of lipid composition

Our previous short‐term experiment demonstrated that seed oil from bitter melon (Momordica charantia) (BMO), which is rich in cis(c)9, trans(t)11, t13‐conjugated linolenic acid (CLN), inhibited the development of azoxymethane (AOM)‐induced colonic aberrant crypt foci (ACF). In our study, the possible inhibitory effect of dietary administration of BMO on the development of colonic neoplasms was investigated using an animal colon carcinogenesis model initiated with a colon carcinogen AOM. Male F344 rats were given subcutaneous injections of AOM (20 mg/kg body weight) once a week for 2 weeks to induce colon neoplasms. They also received diets containing 0.01%, 0.1% or 1% BMO for 32 weeks, starting 1 week before the first dosing of AOM. At the termination of the study (32 weeks), AOM induced 83% incidence (15/18 rats) of colonic adenocarcinoma. Dietary supplementation with 0.01% and 0.1% BMO caused significant reduction in the incidence (47% inhibition by 0.01% BMO, p<0.02; 40% inhibition by 0.1% BMO, p<0.05; and 17% inhibition by 1% BMO) and the multiplicity (64% inhibition by 0.01% BMO, p<0.005; 58% inhibition by 0.1% BMO, p<0.02; and 48% inhibition by 1% BMO, p<0.05) of colonic adenocarcinoma, though a clear dose response was not observed. Such inhibition was associated with the increased content of CLA (c9,t11‐18:2) in the lipid composition in colonic mucosa and liver. Also, BMO administration in diet enhanced expression of peroxisome proliferator‐activated receptor (PPAR) γ protein in the nonlesional colonic mucosa. These findings suggest that BMO rich in CLN can suppress AOM‐induced colon carcinogenesis and the inhibition might be caused, in part, by modification of lipid composition in the colon and liver and/or increased expression of PPARγ protein level in the colon mucosa. © 2004 Wiley‐Liss, Inc.
RANTES (regulated on activation, normal T cell expressed and secreted), inflammation, obesity, and the metabolic syndrome.

For a long time, white adipose tissue (WAT) has been regarded as an inert tissue for energy storage. With the rapidly rising incidence of the components of the metabolic syndrome—obesity, diabetes mellitus type II, and hypertension—in the industrialized world, these diseases have attracted increasing attention in research and health politics. In parallel, WAT was recognized as an active endocrine and paracrine organ that plays an important role in the metabolic syndrome.1 Article p 1029 Various studies within the past decade indicated that WAT in obesity is characterized by a chronic low-grade inflammation with secretion of inflammatory cytokines and chemokines (see the Figure). Tumor necrosis factor-α was identified as the first molecular link between inflammation and obesity by Hotamisligil and coworkers: Expression of this cytokine was increased in WAT of obese mice2 and correlated with obesity-induced insulin resistance.3 Interleukin-6 (IL-6) is another cytokine critically involved in the pathogenesis of obesity and insulin resistance. The serum levels of IL-6 positively correlate with obesity in humans and predict the risk of development of insulin resistance and diabetes mellitus type 2.4 IL-6 is produced by a variety of metabolic tissues that include WAT, hepatocytes, β-cells, and skeletal muscle. Thus, circulating IL-6 could mediate a crosstalk between these organs that results in a downward spiral toward systemic insulin resistance and decreased insulin secretion.5 Furthermore, obesity was found to be associated with macrophage accumulation in murine and human WAT.6 Chemokines such as CCL2/monocyte chemoattractant protein-1 (MCP-1) and CCL3/macrophage inflammatory protein-1α were reported to be increased in WAT of obese mice and to contribute to insulin resistance and macrophage recruitment.7 Recently, a causal relationship between obesity, WAT inflammation, and insulin resistance was characterized for MCP-1 and its receptor CCR2: MCP-1 enhanced macrophage infiltration in WAT, insulin resistance, and hepatic steatosis …
Song retuning with tutor model by adult zebra finches

Songbirds first memorize a tutor song in youth and develop their own song after the remembered model. As birds sexually mature, their song becomes crystallized and refractory to further tutoring. Here, we show that the song syllables of adult zebra finches gradually drift from their once crystallized forms, when individual birds are kept in auditory isolation or in company of cage mates singing different song syllables. Furthermore, when birds with drifted syllables are tutored with the same model again, they amend the fine structure of their syllables towards the model. In contrast, retutoring does not affect syllable sequences that differ from those of the original tutor. © 2008 Wiley Periodicals, Inc. Develop Neurobiol 2008
Protein tyrosine phosphatase TbPTP1: a molecular switch controlling life cycle differentiation in trypanosomes

Differentiation in African trypanosomes (Trypanosoma brucei) entails passage between a mammalian host, where parasites exist as a proliferative slender form or a G0-arrested stumpy form, and the tsetse fly. Stumpy forms arise at the peak of each parasitaemia and are committed to differentiation to procyclic forms that inhabit the tsetse midgut. We have identified a protein tyrosine phosphatase (TbPTP1) that inhibits trypanosome differentiation. Consistent with a tyrosine phosphatase, recombinant TbPTP1 exhibits the anticipated substrate and inhibitor profile, and its activity is impaired by reversible oxidation. TbPTP1 inactivation in monomorphic bloodstream trypanosomes by RNA interference or pharmacological inhibition triggers spontaneous differentiation to procyclic forms in a subset of committed cells. Consistent with this observation, homogeneous populations of stumpy forms synchronously differentiate to procyclic forms when tyrosine phosphatase activity is inhibited. Our data invoke a new model for trypanosome development in which differentiation to procyclic forms is prevented in the bloodstream by tyrosine dephosphorylation. It may be possible to use PTP1B inhibitors to block trypanosomatid transmission.
Multi-User Detection for Spatial Modulation via Structured Approximate Message Passing

In this letter, we propose an efficient structured approximate message passing (Str-AMP) detector for multi-user spatial modulation systems. Str-AMP consists of two steps in each iteration. First, a decoupling operation is performed in the same way as AMP. Then, at the denoising step, to exploit the structured sparsity of SM signals, Str-AMP computes each element of SM signals using not only its own statistics but also those of its neighboring elements belonging to the same user. Since Str-AMP maintains scalar message passing, it is computationally efficient. Simulation results on various settings demonstrate the superiority of the proposed Str-AMP in terms of both uncoded and coded bit error rate performance.
Using a Different Model for Female Sexual Response to Address Women's Problematic Low Sexual Desire

An intimacy-based sex response cycle was used in the assessment of 47 women referred with low sexual desire. All could relate to the model and multiple breaks in the cycles were identified. Emotional intimacy to motivate the women to find sexual stimuli to elicit arousal was insufficient in 50%. Sexual stimuli and context were minimal in 53%. Psychological factors diminishing arousability were identified in 85%, depression contributing in 43%. Androgen deficiency (the cause suggested by referring doctors) contributed in 25%. Identifying missing components of their "normal" but currently problematic sex response cycles was itself therapeutic.
Functional Connectivity of the Caudal Anterior Cingulate Cortex Is Decreased in Autism

The anterior cingulate cortex (ACC) is frequently reported to have functionally distinct sub-regions that play key roles in different intrinsic networks. However, the contribution of the ACC, which is connected to several cortical areas and the limbic system, to autism is not clearly understood, although it may be involved in dysfunctions across several distinct but related functional domains. By comparing resting-state fMRI data from persons with autism and healthy controls, we sought to identify the abnormalities in the functional connectivity (FC) of ACC sub-regions in autism. The analyses found autism-related reductions in FC between the left caudal ACC and the right rolandic operculum, insula, postcentral gyrus, superior temporal gyrus, and the middle temporal gyrus. The FC (z-scores) between the left caudal ACC and the right insula was negatively correlated with the Stereotyped Behaviors and Restricted Interests scores of the autism group. These findings suggest that the caudal ACC is recruited selectively in the pathomechanism of autism.
Self-Organized Behavior Generation for Musculoskeletal Robots

With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors “waiting” to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics.
Investigations on the growth, structural, optical, mechanical, dielectric and SHG behaviour of GPMG crystals

Abstract Glycinium picrate mono glycine crystals have been grown by slow evaporation solution technique and Sankaranarayanan–Ramasamy (SR) method. The size of the grown crystal in slow evaporation method was 15 × 3 × 2 mm3 and in SR method it was 15 mm in diameter and 38 mm in length. The grown crystals were subjected to crystal structure, single crystal X-ray diffraction, powder X-ray diffraction, High Resolution X-ray diffraction, Etching, UV–Vis, dielectric, mechanical and non-linear optical studies. The crystals grown by SR method have 90% of transmittance and the crystals grown by slow evaporation method has 65% of transmittance. In order to determine mechanical strength of crystal, Vickers micro-hardness measurement was carried out. SR method grown crystals has higher hardness. Dielectric study reveals higher dielectric constant and low dielectric loss for SR method grown crystal. The second harmonic efficiency of grown crystal is higher compared to pure KDP.
Acute gout at engraftment following hematopoietic transplantation

Anemia is a symptom associated with cognitive dysfunction and is diagnosed if the hemoglobin level of a blood sample is too low. The clinical impact of chronically low hemoglobin level may be insufficient brain oxygenation, which may result in a decline in cognitive functioning. Previous studies have provided evidence of decrements in cognitive functioning associated with anemia across various disease processes, but few have investigated the association between cognitive dysfunction and hemoglobin level in patients with acute myelogenous leukemia (AML) and myelodysplastic syndrome (MDS). As this population is inherently anemic, studying these patients allowed for an exploration of cognitive changes at mild, moderate, and severe levels of anemia. This investigation explored cutoff points for hemoglobin at which cognitive decline may occur. Findings showed decrements in cognitive functioning occurring at hemoglobin levels of 10 g/dL or below. Performance on measures of word retrieval, attention, and fine motor function was most affected which suggests fronto-temporal lobe dysfunction. Results provided evidence as to a hemoglobin cutoff point below which cognitive function may be affected in patients with AML and MDS. This cutoff value may provide a clinical marker at which cognitive testing and therapeutic interventions could be utilized to improve patients’ cognitive function, level of fatigue and overall quality of life.
A Secure Group Key Management Protocol Communication Lower Bound

We discuss in this paper a lower bound on communication cost for secure group key management protocols. To model a rekeying process, we introduce the concept of rekey encryption graphs. Using the rekey encryption graphs, we show that given the forward secrecy requirement, i.e. a user who has left the secure group cannot have access to future group keys, there exists a sequence of user join and leave requests such that the amortized per request communication cost is . Given the known protocols that have achieved this lower bound, in order to further improve the scalability of group rekeying communication protocol performance, future research needs to allow more types of operations to achieve better performance.
Learning to Log: Helping Developers Make Informed Logging Decisions

Logging is a common programming practice of practical importance to collect system runtime information for postmortem analysis. Strategic logging placement is desired to cover necessary runtime information without incurring unintended consequences (e.g., Performance overhead, trivial logs). However, in current practice, there is a lack of rigorous specifications for developers to govern their logging behaviours. Logging has become an important yet tough decision which mostly depends on the domain knowledge of developers. To reduce the effort on making logging decisions, in this paper, we propose a "learning to log" framework, which aims to provide informative guidance on logging during development. As a proof of concept, we provide the design and implementation of a logging suggestion tool, Log Advisor, which automatically learns the common logging practices on where to log from existing logging instances and further leverages them for actionable suggestions to developers. Specifically, we identify the important factors for determining where to log and extract them as structural features, textual features, and syntactic features. Then, by applying machine learning techniques (e.g., Feature selection and classifier learning) and noise handling techniques, we achieve high accuracy of logging suggestions. We evaluate Log Advisor on two industrial software systems from Microsoft and two open-source software systems from Git Hub (totally 19.1M LOC and 100.6K logging statements). The encouraging experimental results, as well as a user study, demonstrate the feasibility and effectiveness of our logging suggestion tool. We believe our work can serve as an important first step towards the goal of "learning to log".
Asymptomatic Severe Vagal and Sympathetic Cardiac Denervation in Holmes-Adie's Syndrome

A 40-year-old woman was found to have bilateral Adie's pupils and generalized muscle stretch areflexia. She did not have orthostatic hypotension but, in an ECG strip in the office, she appeared to have an almost fixed heart rate. We thus studied the heart rate variability (HRV) and the systolic blood pressure variability (SBPV) in supine and standing position and also during rhythmic breathing. We found a decreased HRV in the time domain with very low standard deviation in supine and standing position and during rhythmic breathing. HRV in the frequency domain was low with a decrease in the absolute power of HF and LF and a decrease in the sympathovagal balance in supine and standing positions. SBPV in the time and frequency domains was found to be normal. This patient with Holmes-Adie syndrome had an asymptomatic severe loss of HRV and a preserved SBPV. The global decrease in the HRV in the time and frequency domains indicated that she had both vagal and sympathetic cardiac denervation, whereas the preserved SBPV suggested normal innervation of the blood vessels.