Miracle-dz/UniFAR-FTUs huggingface dataset:
A common dimerization interface in bacterial response regulators KdpE and TorR

Bacterial response regulators are key regulatory proteins that function as the final elements of so‐called two‐component signaling systems. The activities of response regulators in vivo are modulated by phosphorylation that results from interactions between the response regulator and its cognate histidine protein kinase. The level of response regulator phosphorylation, which is regulated by intra‐or extracellular signals sensed by the histidine protein kinase, ultimately determines the output response that is initiated or carried out by the response regulator. We have recently hypothesized that in the OmpR/PhoB subfamily of response regulator transcription factors, this activation involves a common mechanism of dimerization using a set of highly conserved residues in the α4–β5–α5 face. Here we report the X‐ray crystal structures of the regulatory domains of response regulators TorR (1.8 Å), Ca2+‐bound KdpE (2.0 Å), and Mg2+/BeF3−‐bound KdpE (2.2 Å), both members of the OmpR/ PhoB subfamily from Escherichia coli. Both regulatory domains form symmetric dimers in the asymmetric unit that involve the α4–β5–α5 face. As observed previously in other OmpR/PhoB response regulators, the dimer interfaces are mediated by highly conserved residues within this subfamily. These results provide further evidence that most all response regulators of the OmpR/ PhoB subfamily share a common mechanism of activation by dimerization.
The PANDORA project: A success story in AUV autonomy

This paper presents some of the results of the EU-funded project PANDORA - Persistent Autonomy Through Learning Adaptation Observation and Re-planning. The project was three and a half years long and involved several organisations across Europe. The application domain is underwater inspection and intervention, a topic particularly interesting for the oil and gas sector, whose representatives constituted the Industrial Advisory Board. Field trials were performed at The Underwater Centre, in Loch Linnhe, Scotland, and in harbour conditions close to Girona, Spain.
Miniature Endplate Current Kinetics at the Mouse Neuromuscular Junction: Effects of Temperature and Medium Viscosity

The time course of miniature endplate currents (MEPCs), derived by extracellular focal recording, was studied in the mouse neuromuscular junction at different temperatures and medium viscosities, and in eserine‐treated endplates. At low temperatures (6–10°C), almost the whole MEPC decay is exponential and the rising phase is not significantly modified by the channel closing process. At physiological temperatures (38–40°C), the early part of the decay is much slower than the later part and the rising phase is made shorter and smaller by channel closing, showing that the channel opening and channel closing processes overlap remarkably. Even at physiological temperatures, however, the late part of MEPC decay shows an exponential time course. At high temperatures the channel opening process has low temperature sensitivity and slows down when bath solution viscosity is increased, suggesting that at high temperatures channel opening kinetics may mainly be controlled by the time course of acetylcholine diffusion. The lower limit of conformational change rate leading to channel opening was estimated at 10°C (4400 s‐1). Experimentally recorded MEPCs were mathematically simulated to obtain a quantitative description of the processes controlling MEPC generation. Mathematical simulation further suggests that (i) acetylcholine diffusion kinetics may affect the onset rate of MEPCs without, however, being rate‐limiting; and (ii) partial, transient acetylcholinesterase inhibition operated by acetylcholine may explain the low temperature sensitivity exhibited by the onset rate of MEPCs at high temperatures.
Can Aidi injection restore cellular immunity and improve clinical efficacy in non-small-cell lung cancer patients treated with platinum-based chemotherapy? A meta-analysis of 17 randomized controlled trials following the PRISMA guidelines

Background:Aidi injection is an adjuvant chemotherapy drug commonly used in China. Can Aidi injection restore the cellular immunity and improve the clinical efficacy in non-small-cell lung cancer (NSCLC) patients treated with platinum-based chemotherapy? There is a lack of strong evidence to prove it. To further reveal it, we systematically evaluated all related studies. We collected all studies about the clinical efficacy and cellular immunity of Aidi injection plus platinum-based chemotherapy for NSCLC in Medline, Embase, Web of Science, China national knowledge infrastructure database (CNKI), Chinese Scientific Journals Full-Text Database (VIP), Wanfang, China biological medicine database (CBM) (established to June 2015), Cochrane Central Register of Controlled Trials (CCRCT) (June 2015), Chinese clinical trial registry, and US-clinical trials (June 2015). We evaluated their quality according to the Cochrane evaluation handbook of randomized controlled trials (RCTs) (5.1.0), extracted data following the patient intervention control group outcomes principles and synthesized the data by meta-analysis. Seventeen (RCTs) with 1390 NSCLC patients were included, with general methodological quality in most trials. The merged relative risk (RR) values and their 95% CI of meta-analysis for objective response rate (ORR) and disease control rate (DCR) were as follows: 1.26 (1.12, 1.42) and 1.11(1.04, 1.17). The merged standardized mean difference (SMD) values and their 95% CI of meta-analysis for the percentage of CD3+T cells, CD4+T cells, CD8+T cells, natural killer (NK) cells, and CD4+/CD8+ T cell ratio were as follows: 1.41, (0.89, 1.92), 1.59, (1.07, 2.11), 0.85, (0.38, 1.33), 1.64 (0.89, 2.39) and 0.91, (0.58, 1.24). Compared with platinum-based chemotherapy alone, all differences were statistically significant. These results might be overestimated or underestimated. Conclusions:Aidi injection plus platinum-based chemotherapy can improve the clinical efficacy of patients with NSCLC. Aidi injection could significantly restore the cellular immunity damaged by platinum-based chemotherapy. It may be an important tumor immune modulator and protector for patients with NSCLC treated with chemotherapy.
Monitoring Model on Diffusion Law Identification of Network Public Opinion for Major Public Crisis

Network communication technology develops in the form of fission,the Internet forms"free market" of public opinion.Therefore,to identify the diffusion law of network public opinion and guide has the growing importance.Based on"Six Degrees of Separation" hypothesis,small-world network and scale-free networks,the thesis analyzes information diffusion evolution process of network public opinion for unexpected major public crisis,and also constructs an Agent-based network monitoring model for diffusion process of public opinion and its corresponding diffusion-law analyzing model.The simulation results are consistent with the actual situation.It is significant to resolve social contradictions,to solve a public crisis,and to build a harmonious society.
Deposition of dietary fatty acids, de novo synthesis and anatomical partitioning of fatty acids in finishing pigs

Predicting aspects of pork quality becomes increasingly important from both a nutritional and technological point of view. The aim of the present study was to provide quantitative information on the relation between nutrient intake and whole-body fatty acid (FA) deposition. This information is essential to develop mechanistic models predicting the FA content of tissues. A serial slaughter study was carried out in which thirty pigs were slaughtered between 90 and 150 kg. The diet included 15 g/kg soyabean oil and contained 44 g/kg fat. Only 0·31 and 0·40 of the digested n-6 and n-3 FA were deposited, respectively. Approximately one-third of the n-3 supply that was deposited resulted from the conversion of 18 : 3 to other metabolites (i.e. EPA, docosapentaenoic acid and DHA). This proportion was affected by the pig genotype. De novo-synthesised FA represented 0·86 of the total non-essential FA deposition, and its average composition corresponded to 0·017, 0·286, 0·025, 0·217 and 0·454 for 14 : 0, 16 : 0, 16 : 1, 18 : 0 and 18 : 1, respectively. Although the average whole-body FA composition was relatively constant during the finishing period, this was not so for the tissues. In the carcass (without backfat), the content of 18 : 1 increased during the finishing period, whereas that of 16 : 0 and 18 : 0 decreased. Backfat captured a proportionally greater fraction of 18 : 2 than did the carcass or the residual tissues. In contrast, a proportionally greater fraction of the dietary 18 : 3 supply was deposited in the carcass compared to other tissues.
Pretreatment Tumor Thickness as a Predictor of Pathologic Complete Response to Neoadjuvant Chemoradiation Therapy for Stage II/III Rectal Adenocarcinoma

Objectives: To evaluate pretreatment tumor thickness in predicting pathologic complete response (pCR) of stage II/III rectal adenocarcinoma to neoadjuvant chemoradiation (chemoradiotherapy [CRT]). Methods: We retrospectively analyzed 185 patients who were diagnosed with stage II or III rectal adenocarcinoma from January 2011 to July 2013 and treated with neoadjuvant intensity-modulated radiation therapy (45 Gy in 1.8-Gy fractions to pelvis and 50 Gy in 2-Gy fractions to rectal tumor as an integrated boost) or 3 dimensionally conformal radiation therapy (45 Gy in 1.8-Gy fractions to pelvis followed by an additional 5.4-Gy to rectal tumor) concurrently with two 3-week cycles of chemotherapy (oxaliplatin 130 mg/m2 on day 1 and capecitabine 825 mg/m2, twice per day from day 1 to 14, cycle 2 starts on week 4). One week after CRT, 36% patients received 1 more cycle of the above chemotherapy and 55% received 1 to 2 cycles of FOLFOX6. Tumor response was categorized as pCR and non-pCR. Tumor thickness measured on magnetic resonance imaging was collected. A multivariate logistic regression model was used to evaluate the association of potential predictors and pCR. Results: Thirty-eight patients (20.5%) reached pCR. Multivariate analysis found the pretreatment tumor thickness to be associated with higher probability of pCR after adjusting for radiation therapy-surgery interval time and pretreatment carcino-embryonic antigen level. The pretreatment carcino-embryonic antigen level was associated with pCR in the univariate analysis but lost the association in the multivatiate model. The pretreatment T or N stage, tumor volume, distance from tumor to anal verge, craniocaudal length of tumor, radiation therapy technique, and patient age and sex were not associated with pCR. Conclusions: We concluded that pretreatment tumor thickness is an independent predictor for pCR of stage II/III rectal adenocarcinoma to the neoadjuvant CRT.
Music Training and Education Slow the Deterioration of Music Perception Produced by Presbycusis in the Elderly

The perception of music depends on the normal function of the peripheral and central auditory system. Aged subjects without hearing loss have altered music perception, including pitch and temporal features. Presbycusis or age-related hearing loss is a frequent condition in elderly people, produced by neurodegenerative processes that affect the cochlear receptor cells and brain circuits involved in auditory perception. Clinically, presbycusis patients have bilateral high-frequency hearing loss and deteriorated speech intelligibility. Music impairments in presbycusis subjects can be attributed to the normal aging processes and to presbycusis neuropathological changes. However, whether presbycusis further impairs music perception remains controversial. Here, we developed a computerized version of the Montreal battery of evaluation of amusia (MBEA) and assessed music perception in 175 Chilean adults aged between 18 and 90 years without hearing complaints and in symptomatic presbycusis patients. We give normative data for MBEA performance in a Latin-American population, showing age and educational effects. In addition, we found that symptomatic presbycusis was the most relevant factor determining global MBEA accuracy in aged subjects. Moreover, we show that melodic impairments in presbycusis individuals were diminished by music training, while the performance in temporal tasks were affected by the educational level and music training. We conclude that music training and education are important factors as they can slow the deterioration of music perception produced by age-related hearing loss.
Fam57b (Family with Sequence Similarity 57, Member B), a Novel Peroxisome Proliferator-activated Receptor γ Target Gene That Regulates Adipogenesis through Ceramide Synthesis*

Background: Fam57b was identified as a putative novel PPARγ target up-regulated in adipocytes and adipose tissue. Results: Fam57b was confirmed as a novel target of PPARγ by reporter and ChIP assays. FAM57B synthesizes ceramides and inhibits adipogenesis in mouse stromal ST2 cells. Conclusion: FAM57B regulates adipogenesis through ceramide synthesis. Significance: This study reveals one of the pleiotropic actions of PPARγ related to ceramide metabolism. This report identifies a novel gene encoding Fam57b (family with sequence similarity 57, member B) as a novel peroxisome proliferator-activated receptor γ (PPARγ)-responsive transmembrane gene that is related to obesity. The gene was identified based on an integrated bioinformatics analysis of the following three expression profiling data sets: adipocyte differentiation of mouse stromal cells (ST2 cells), adipose tissues from obesity mice, and siRNA-mediated knockdown of Pparγ using ST2 cells. Fam57b consists of three variants expressed from different promoters and contains a Tram-Lag1-CLN8 domain that is related to ceramide synthase. Reporter and ChIP assays showed that Fam57b variant 2 is a bona fide PPARγ target gene in ST2 cells. Fam57b was up-regulated during adipocyte differentiation, suggesting that FAM57B is involved in this process. Surprisingly, FAM57B overexpression inhibited adipogenesis, and siRNA-mediated knockdown promoted adipocyte differentiation. Analysis of the ceramide content by lipid assay found that ceramides were in fact augmented in FAM57B-overexpressing ST2 cells. We also confirmed that ceramide inhibits adipogenesis. Therefore, the aforementioned results of FAM57B overexpression and siRNA experiments are reconciled by ceramide synthesis. In summary, we present in vitro evidence showing that PPARγ regulates Fam57b transcription during the adipogenesis of ST2 cells. In addition, our results suggest that PPARγ activation contributes to the regulation of ceramide metabolism during adipogenesis via FAM57B.
Nup53p is a Target of Two Mitotic Kinases, Cdk1p and Hrr25p

Nuclear pore complexes (NPCs) form channels across the nuclear envelope and provide the sole sites of molecular exchange between the cytoplasm and nucleoplasm. The NPC is a target of a number of post‐translational modifications, including phosphorylation, yet the functions of these modifications are ill defined. Here, we have investigated the mitotic specific phosphorylation of a yeast nucleoporin Nup53p. Two kinases were identified that phosphorylate Nup53p: the mitotic kinase Cdk1p/Cdc2p/Cdc28p and the casein kinase Hrr25p. Hrr25p was identified by screening 119 yeast kinases for their ability to phosphorylate Nup53p in vitro. Conditional alleles of Hrr25p support the conclusion that Hrr25p phosphorylates Nup53p in vivo. We further demonstrated using solution binding and affinity purification assays, that Hrr25p directly binds Nup53p in an interaction that is destabilized by the phosphorylation of Nup53p. Consistent with this observation, we observed that Hrr25p moves between distinct locations in the cell during the cell cycle including the nucleus, the cortex of the emerging bud and the spindle pole bodies. Cdk1p also contributes to Nup53p phosphorylation as specific inhibition of Cdk1p or mutation of Cdk1p consensus sites partially blocked its phosphorylation. The ability of nup53 alleles containing Cdk1p site mutations to complement synthetic defects of nup53Δnup170Δ strains is linked to a function for Nup53p in the spindle assembly checkpoint.
Mechanism of adhesion and detachment at the anterior end of Merizocotyle icopae (Monogenea: Monocotylidae) including ultrastructure of the anterior adhesive matrix

The anterior adhesive mechanism was studied for Merizocotyle icopae (Monogenea: Monocotylidae). Adult anterior apertures can open and close. In addition, duct endings terminating within the apertures are everted or retracted depending on the stage of attachment. Adhesive in adults is synthesized from all 3 secretory types (rod-shaped, small and large spheroidal bodies) found within anterior apertures. All exit together and undergo mixing to produce the adhesive matrix, a process that depletes duct contents. A greater number of ducts carrying rod-shaped bodies is depleted than ducts containing spheroidal bodies which changes the ratio of secretory types present on detachment. Detachment involves elongation of duct endings and secretion of additional matrix as the worm pulls away from the substrate. The change in secretory type ratio putatively modifies the properties of the secreted matrix enabling detachment. Only after detachment do ducts refill. During attachment, individual secretory bodies undergo morphological changes. The larval and adult adhesive matrix differs. Anterior adhesive in oncomiracidia does not show fibres with banding whereas banded fibres comprise a large part of adult adhesive. The data suggest that this is the result of adult spheroidal secretions modifying the way in which the adult adhesive matrix forms.
Multifactor dimensionality reduction analysis of MTHFR, PAI-1, ACE, PON1, and eNOS gene polymorphisms in patients with early onset coronary artery disease

Background: Association studies in the Turkish population have investigated the single locus effects of different gene polymorphisms on coronary artery disease (CAD). CAD is a complex polygenic disease that involves complex interactions among multiple genetic and environmental conditions. Design: We evaluated associations of five candidate genetic polymorphisms (methylene tetrahydrofolate reductase C677T, plasminogen activator inhibitor 4G/5G, endothelial nitric oxide synthase (eNOS) 3–27 base pair repeat, insertion, or deletion of a 287 bp Alu repeat sequence polymorhism of angiotensin I converting enzyme, and paraoxonase Gln192Arg PON1 polymorphisms) with the presence and extent of early onset CAD. Methods: DNA was isolated and amplified from 90 consecutive patients with angiographically proven early onset CAD (ages 41 ± 5 for men, 49 ± 7 for women) and also from 90 control subjects with no significant coronary obstruction angiographically (ages 42 ± 5 for men, 48 ± 6 for women). Multifactor dimensionality reduction (MDR) analysis was performed to identify a model of CAD based on both genetic and conventional risk factors. Results: MDR analysis detected a significant model with four genes (prediction success ∼ 61%, p = 0.03). When the total number of the conventional risk factors is analysed with the candidate polymorphisms, a different model is identified that includes three of the four genes from the above model and achieves a similar prediction of CAD as the gene only model. Conclusion: These data indicate that gene–gene and gene–environmental risk interactions form significant models in predicting early onset CAD.
Types of Suggestibility: Relationships Among Compliance, Indirect, and Direct Suggestibility

Abstract It is commonly believed that direct suggestibility, referring to overt influence, and indirect suggestibility, in which the intention to influence is hidden, correlate poorly. This study demonstrates that they are substantially related, provided that they tap similar areas of influence. Test results from 103 students, 55 women and 48 men, were entered into regression analyses. Indirect suggestibility, as measured by the Sensory Suggestibility Scale for Groups, and compliance, measured by the Gudjonsson Compliance Scale, were predictors of direct suggestibility, assessed with the Barber Suggestibility Scale. Spectral analyses showed that indirect suggestibility is more related to difficult tasks on the BSS, but compliance is more related to easy tasks on this scale.
A new approach for isolating cell wall mutants in Saccharomyces cerevisiae by screening for hypersensitivity to calcofluor white

To study cell wall assembly, a simple screening method was devised for isolating cell wall mutants. Mutagenized cells were screened for hypersensitivity to Calcofluor White, which interferes with cell wall assembly. The rationale is that Calcofluor White amplifies the effect of cell wall mutations. As a result, the cells stop growing at lower concentrations of Calcofluor White than cells with normal cell wall. In this way, 63 Calcofluor White‐hypersensitive (cwh), monogenic mutants were obtained, ordered into 53 complementation groups.
Risk Factors of Posttraumatic Stress Disorder After an Earthquake Disaster

Abstract This study sought to predict posttraumatic stress disorder (PTSD) from women’s reproductive health events after an earthquake experience. Data on antenatal care, pregnancy outcomes, family planning, socioeconomic status, earthquake experiences, and mental health were collected from a random sample of 425 women of reproductive age using the Centers for Disease Control and Prevention Reproductive Health Assessment Toolkit and the Harvard Trauma Questionnaire. Data were analyzed using multivariate regression analysis to predict PTSD symptoms from posttrauma care variables and reproductive health events. Restricted social participation, use of temporary accommodation, pregnancy complications, and use of injectable contraceptives were significant risk factors of PTSD. These factors may be exacerbated by the social context of conservative societies, traditions about health care–seeking behavior, and access to health care. Antecedent reproductive health events influence women’s reaction to major trauma including events such as an earthquake.
Comparative analysis of the Bluetooth Low-Energy indoor positioning systems

A key requirements in the Internet of Things (IoT) concept are context-aware computation, smart connectivity with existing networks and cost efficient low-power wireless solutions. Bluetooth Low Energy (BLE) is one of the latest developments of IoT and especially well-suited for ultra-low power sensors running on small batteries. BLE is successful alternative for indoor positioning systems (IPS) which offers reasonable accuracy and low cost deployment. This paper presents a comparative analysis of contemporary BLE indoor positioning solutions, taking into account the classification, comparison and variety considerations of parameters that are required for designing a new indoor positioning approaches.