Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Salmonella enterica Serovar Typhimurium mntH Transcription by H2O2, Fe2+, and Mn2+

ABSTRACT MntH, a bacterial homolog of mammalian natural resistance associated macrophage protein 1 (Nramp1), is a primary transporter for Mn2+ influx in Salmonella enterica serovar Typhimurium and Escherichia coli. S. enterica serovar Typhimurium MntH contributes to H2O2 resistance and is important for full virulence. Consistent with its phenotype and function, mntH is regulated at the transcriptional level by both H2O2 and substrate cation. We have now identified three trans-acting regulatory factors and the three corresponding cis-acting mntH promoter motifs that mediate this regulation. In the presence of hydrogen peroxide, mntH is activated by OxyR, acting through an OxyR-binding motif centered just upstream of the likely −35 RNA polymerase-binding site. In the presence of Fe2+, mntH is repressed primarily by Fur, acting through a Fur-binding motif overlapping the −35 region. In the presence of Mn2+, mntH is repressed primarily by the Salmonella equivalent of E. coli b0817, a distant homolog of the Bacillus subtilis manganese transport repressor, MntR, acting through an inverted-repeat motif located between the likely −10 polymerase binding site and the ribosome binding site. E. coli b0817 was recently shown to bind the identical inverted-repeat motif in the E. coli mntH promoter and hence has been renamed MntR (S. I. Patzer and K. Hantke, J. Bacteriol. 183:4806-4813, 2001). Using Δfur, ΔmntR, and Δfur ΔmntR mutant strains as well as mutations in the Fur- and MntR-binding motif elements, we found that Fe2+ can also mediate repression through the Mn2+ repressor MntR.
Influence of NRGN rs12807809 polymorphism on symptom severity in individuals with schizophrenia in the Han population but not the Zhuang population of south China

Background NRGN is one of the most promising candidate genes for schizophrenia based on function and position. Therefore, this study aimed to examine the genetic association of this polymorphism with schizophrenia in the Zhuang and Han populations of south China. Subjects and methods A total of 282 patients (188 Han and 94 Zhuang) and 282 healthy subjects (188 Han and 94 Zhuang) were recruited. Of these, 246 schizophrenia patients underwent an assessment of psychotic symptoms using the Positive and Negative Syndrome Scale (PANSS). A TaqMan genotyping assay method was used to determine the genotypes. Results We did not find a significant association of rs12807809 polymorphism with schizophrenia in the total pooled samples, or in the separate ethnic groups. However, in Han schizophrenia patients, quantitative data analyses showed that the CC genotype of the rs12807809 polymorphism was associated with PANSS aggression subscale score and activation subscale score. Furthermore, carriers of the C allele of rs12807809 polymorphism among Han schizophrenia patients had higher scores of general, activation, depression, aggression, and global symptoms than the T allele carriers. Conclusion In conclusion rs12807809 polymorphism may not contribute to the risk of schizophrenia but influence the clinical symptoms of schizophrenia in the Han population.
Increased amygdala: hippocampal volume ratios associated with severity of anxiety in pediatric major depression.

BACKGROUND Neurobiologic abnormalities in the temporal lobe, particularly medial temporolimbic circuits, have been implicated in the pathogenesis of major depressive disorder (MDD). Although MDD commonly emerges during childhood and adolescence, to our knowledge, no prior study has examined temporal lobe anatomy in pediatric patients with MDD near the onset of illness before treatment. METHODS Volumetric magnetic resonance imaging scans were conducted in 23 psychotropic drug-naïve pediatric patients with MDD, aged 8-17 years, and 23 case-matched healthy comparison subjects. RESULTS Pediatric patients with MDD had significantly larger left (14%) and right (11%) amygdala:hippocampal volume ratios than controls. Increased left and right amygdala:hippocampal volume ratios were associated with increased severity of anxiety but not increased severity of depression or duration of illness. CONCLUSION These results suggest that alterations in amygdala:hippocampal volume ratios in pediatric MDD may more reflect severity of associated anxiety than depression. These results underscore the importance of assessment for comorbidity in the study of MDD.
Automatic feature point detection and tracking of human actions in time-of-flight videos

Detecting feature points on the human body in video frames is a key step for tracking human movements. There have been methods developed that leverage models of human pose and classification of pixels of the body image. Yet, occlusion and robustness are still open challenges. In this paper, we present an automatic, model-free feature point detection and action tracking method using a time-of-flight camera. Our method automatically detects feature points for movement abstraction. To overcome errors caused by miss-detection and occlusion, a refinement method is devised that uses the trajectory of the feature points to correct the erroneous detections. Experiments were conducted using videos acquired with a Microsoft Kinect camera and a publicly available video set and comparisons were conducted with the state-of-the-art methods. The results demonstrated that our proposed method delivered improved and reliable performance with an average accuracy in the range of 90 U+0025. The trajectory-based refinement also demonstrated satisfactory effectiveness that recovers the detection with a success rate of 93.7 U+0025. Our method processed a frame in an average time of 71.1 ms.
The effect of pre-operative psychological interventions on post-operative outcomes in Chinese women having an elective hysterectomy.

OBJECTIVE To test the effect of cognitive interventions with information given pre-operatively on post-operative outcomes in Chinese women undergoing elective hysterectomies. DESIGN An experimental design. The experimental group (n=48) received cognitive distraction and cognitive reappraisal with information, the control group (n=48) received information only. OUTCOME MEASURES Post-operative anxiety (Chinese State-Trait Anxiety Inventory and mean arterial blood pressure), post-operative requests for analgesia (drug record), post-operative pain (visual analogue scale) and satisfaction (Chinese Patient Satisfaction Questionnaire). RESULTS Cognitive distraction and reappraisal with information produced lower post-operative anxiety and pain scores and higher levels of satisfaction than information only. Post-operative analgesic requests did not differ between groups. CONCLUSIONS Cognitive distraction and reappraisal with information, when used with women undergoing a hysterectomy may have significant clinical benefits.
Prevalence and risk factors of coronary artery disease in patients with chronic viral hepatitis

Abstract Objectives: Patients with chronic viral hepatitis usually present metabolic abnormalities and hemodynamic changes, which are known factors associated with the development of coronary artery disease (CAD). This study aims to determine the risk factors of incident CAD in these patients. Methods: We identified 193 patients who subsequently developed CAD amongst 37,840 cases diagnosed as chronic viral hepatitis from January 2007 through December 2013. Results: In these patients, 141 had hepatitis B virus infections and 52 had hepatitis C virus infections. There was a male preponderance (65.9%). The median age at the diagnosis of hepatitis was 51 years. In the univariate analysis, patients aged ≥ 51 years had shorter median periods from the diagnosis of hepatitis to the onset of CAD than patients aged < 51 years (50 versus 96 months, p < 0.001), and patients with hypertension had shorter median durations compared to those without hypertension (48 versus 96 months, p < 0.001). Statistical significance also existed between patients with different etiologies (p = 0.004). In the multivariate analysis by Cox regression, age at the diagnosis of hepatitis (p < 0.001; hazard ratio (HR), 1.041; 95% CI, 1.027–1.056) and hypertension (with versus without, p < 0.001; HR, 1.925; 95% CI, 1.419–2.611) were revealed. Conclusions: Age at diagnosis of hepatitis and hypertension appeared to be independent risk factors of incident CAD in these patients. This topic deserves further studies.
Complex Structure of the DNA-binding Domain of AdpA, the Global Transcription Factor in Streptomyces griseus, and a Target Duplex DNA Reveals the Structural Basis of Its Tolerant DNA Sequence Specificity*

Background: AdpA regulates over 500 genes in Streptomyces griseus because of its tolerant DNA specificity. Results: The complex structure of the DNA-binding domain of AdpA and a target DNA was solved. Conclusion: Only two arginine residues of the DNA-binding domain of AdpA recognize directly the target DNA sequence. Significance: The complex structure reveals how AdpA acts as a global transcription factor controlling hundreds of genes. AdpA serves as the global transcription factor in the A-factor regulatory cascade, controlling the secondary metabolism and morphological differentiation of the filamentous bacterium Streptomyces griseus. AdpA binds to over 500 operator regions with the consensus sequence 5′-TGGCSNGWWY-3′ (where S is G or C, W is A or T, Y is T or C, and N is any nucleotide). However, it is still obscure how AdpA can control hundreds of genes. To elucidate the structural basis of this tolerant DNA recognition by AdpA, we focused on the interaction between the DNA-binding domain of AdpA (AdpA-DBD), which consists of two helix-turn-helix motifs, and a target duplex DNA containing the consensus sequence 5′-TGGCGGGTTC-3′. The crystal structure of the AdpA-DBD-DNA complex and the mutant analysis of AdpA-DBD revealed its unique manner of DNA recognition, whereby only two arginine residues directly recognize the consensus sequence, explaining the strict recognition of G and C at positions 2 and 4, respectively, and the tolerant recognition of other positions of the consensus sequence. AdpA-DBD confers tolerant DNA sequence specificity to AdpA, allowing it to control hundreds of genes as a global transcription factor.
Temporal integration of loudness in listeners with hearing losses of primarily cochlear origin.

To investigate how hearing loss of primarily cochlear origin affects the loudness of brief tones, loudness matches between 5- and 200-ms tones were obtained as a function of level for 15 listeners with cochlear impairments and for seven age-matched controls. Three frequencies, usually 0.5, 1, and 4 kHz, were tested in each listener using a two-interval, two--alternative forced--choice (2I, 2AFC) paradigm with a roving-level, up-down adaptive procedure. Results for the normal listeners generally were consistent with published data [e.g., Florentine et al., J. Acoust Soc. Am. 99, 1633-1644 (1996)]. The amount of temporal integration--defined as the level difference between equally loud short and long tones--varied nonmonotonically with level and was largest at moderate levels. No consistent effect of frequency was apparent. The impaired listeners varied widely, but most showed a clear effect of level on the amount of temporal integration. Overall, their results appear consistent with expectations based on knowledge of the general properties of their loudness-growth functions and the equal-loudness-ratio hypothesis, which states that the loudness ratio between equal-SPL long and brief tones is the same at all SPLs. The impaired listeners' amounts of temporal integration at high SPLs often were larger than normal, although it was reduced near threshold. When evaluated at equal SLs, the amount of temporal integration well above threshold usually was in the low end of the normal range. Two listeners with abrupt high-frequency hearing losses (slopes > 50 dB/octave) showed larger-than-normal maximal amounts of temporal integration (40 to 50 dB). This finding is consistent with the shallow loudness functions predicted by our excitation-pattern model for impaired listeners [Florentine et al., in Modeling Sensorineural Hearing Loss, edited by W. Jesteadt (Erlbaum, Mahwah, NJ, 1997), pp. 187-198]. Loudness functions derived from impaired listeners' temporal-integration functions indicate that restoration of loudness in listeners with cochlear hearing loss usually will require the same gain whether the sound is short or long.
A finite element approach for modeling photon transport in tissue.

The use of optical radiation in medical physics is important in several fields for both treatment and diagnosis. In all cases an analytic and computable model of the propagation of radiation in tissue is essential for a meaningful interpretation of the procedures. A finite element method (FEM) for deriving photon density inside an object, and photon flux at its boundary, assuming that the photon transport model is the diffusion approximation to the radiative transfer equation, is introduced herein. Results from the model for a particular case are given: the calculation of the boundary flux as a function of time resulting from a delta-function input to a two-dimensional circle (equivalent to a line source in an infinite cylinder) with homogeneous scattering and absorption properties. This models the temporal point spread function of interest in near infrared spectroscopy and imaging. The convergence of the FEM results are demonstrated, as the resolution of the mesh is increased, to the analytical expression for the Green's function for this system. The diffusion approximation is very commonly adopted as appropriate for cases which are scattering dominated, i.e., where mu s >> mu a, and results from other workers have compared it to alternative models. In this article a high degree of agreement with a Monte Carlo method is demonstrated. The principle advantage of the FE method is its speed. It is in all ways as flexible as Monte Carlo methods and in addition can produce photon density everywhere, as well as flux on the boundary. One disadvantage is that there is no means of deriving individual photon histories.
Minimalist Design for Accelerating Convolutional Neural Networks for Low-End FPGA Platforms

Deep neural networks have gained tremendous attention in both the academic and industrial communities due to their performance in many artificial intelligence applications, particularly in computer vision. However, these algorithms are known to be computationally very demanding for both scoring and model learning applications. State-of-the-art recognition models use tens of millions of parameters and have significant memory and computational requirements. These requirements have restricted the users of deep neural network applications to high-end, expensive, and power hungry IoT platforms to penetrate the deep learning markets. This paper presents work at the leading edge intersection of several evolving technologies, including emerging IoT platforms, Deep Learning, and Field-programmable Gate Array (FPGA) computing. We demonstrate a new minimalist design methodology that minimizes the utilization of FPGA resources and can run deep learning algorithms with over 60 million parameters. This makes particularly suitable for resource-constrained, low-end FPGA platforms.
Marine Biodiversity Hotspots and Conservation Priorities for Tropical Reefs

Coral reefs are the most biologically diverse of shallow water marine ecosystems but are being degraded worldwide by human activities and climate warming. Analyses of the geographic ranges of 3235 species of reef fish, corals, snails, and lobsters revealed that between 7.2% and 53.6% of each taxon have highly restricted ranges, rendering them vulnerable to extinction. Restricted-range species are clustered into centers of endemism, like those described for terrestrial taxa. The 10 richest centers of endemism cover 15.8% of the world's coral reefs (0.012% of the oceans) but include between 44.8 and 54.2% of the restricted-range species. Many occur in regions where reefs are being severely affected by people, potentially leading to numerous extinctions. Threatened centers of endemism are major biodiversity hotspots, and conservation efforts targeted toward them could help avert the loss of tropical reef biodiversity.
FtsH, a Membrane-bound ATPase, Forms a Complex in the Cytoplasmic Membrane of Escherichia coli(*)

The FtsH (HflB) protein of Escherichia coli is integrated into the membrane with two N-terminally located transmembrane segments, while its large cytoplasmic domain is homologous to the AAA family of ATPases. The previous studies on dominant negative ftsH mutants raised a possibility that FtsH functions in multimeric states. We found that FtsH was eluted at fractions corresponding to a larger molecular weight than expected from monomeric structure in size-exclusion chromatography. Moreover, treatment of membranes or their detergent extracts with a cross-linker, dithiobis(succinimidyl propionate), yielded cross-linked products of FtsH. To dissect possible FtsH complex, we constructed an FtsH derivative with c-Myc epitope at its C terminus (FtsH-His6-Myc). When membranes prepared from cells in which FtsH-His6-Myc was overproduced together with the normal FtsH were treated with the cross-linker, intact FtsH and in vitro degradation products of FtsH-His6-Myc without the tag were cross-linked with the tagged FtsH protein. Co-immunoprecipitation experiments confirmed the interaction between the FtsH molecules. To identify regions of FtsH required or sufficient for this interaction, we constructed chimeric proteins between FtsH and EnvZ, a protein with a similar topological arrangement, by exchanging their corresponding domains. We found that only the FtsH-EnvZ hybrid protein with an FtsH-derived membrane anchoring domain and an EnvZ-derived cytoplasmic domain caused a dominant ftsH phenotype and was cross-linked with FtsH. We suggest that the N-terminal transmembrane region of FtsH mediates directly the interaction between the FtsH subunits.
CPAP Increases 6-Minute Walk Distance After Lung Resection Surgery

BACKGROUND: The application of CPAP has been used to minimize postoperative pulmonary complications after lung resection surgery. The aim of this study was to quantify both the CPAP effects upon lung function and functional capacity in early postoperative lung resection, as well as to evaluate if CPAP prolongs air leak through the chest drain. METHODS: Thirty patients in the postoperative period of lung resection were allocated into 2 groups: an experimental group, consisting of 15 patients who underwent a 10 cm H2O CPAP, and a 15 patient control group, who performed breathing exercises. Arterial blood gas analysis, peak expiratory flow (PEF), respiratory muscle strength, spirometry, and 6-min walk test (6MWT) were assessed in the preoperative period, and repeated postoperatively on the first and on the seventh day (6MWT was repeated only on the seventh day). RESULTS: Significant increases in PEF, muscle strength, and FEV1 between the first and seventh postoperative day were observed, both in the experimental and in the control group, whereas FVC and PaO2 increased significantly between the first and seventh postoperative day only in the experimental group. The average loss in 6-min walk distance (6MWD) from preoperative to postoperative day 7 in the experimental group was significantly lower than in control group. When comparing the 2 groups, only 6MWD was statistically different (P < .001). There was no air leakage increase through the drain with the early use of CPAP. CONCLUSION: When compared to breathing exercises, CPAP increases the 6MWD in postoperative lung resection patients, without prolonging air leak through the chest drain.
c-Myc Is Required for the Formation of Intestinal Crypts but Dispensable for Homeostasis of the Adult Intestinal Epithelium

ABSTRACT In self-renewing tissues such as the skin epidermis and the bone marrow, Myc proteins control differentiation of stem cells and proliferation of progenitor cell types. In the epithelium of the small intestine, we show that c-Myc and N-Myc are expressed in a differential manner. Whereas c-Myc is expressed in the proliferating transient-amplifying compartment of the crypts, N-Myc is restricted to the differentiated villus epithelium and a single cell located near the crypt base. c-Myc has been implicated as a critical target of the canonical Wnt pathway, which is essential for formation and maintenance of the intestinal mucosa. To genetically assess the role of c-Myc during development and homeostasis of the mammalian intestine we induced deletion of the c-myc flox allele in the villi and intestinal stem cell-bearing crypts of juvenile and adult mice, via tamoxifen-induced activation of the CreERT2 recombinase, driven by the villin promoter. Absence of c-Myc activity in the juvenile mucosa at the onset of crypt morphogenesis leads to a failure to form normal numbers of crypts in the small intestine. However, all mice recover from this insult to form and maintain a normal epithelium in the absence of c-Myc activity and without apparent compensation by N-Myc or L-Myc. This study provides genetic and molecular evidence that proliferation and expansion of progenitors necessary to maintain the adult intestinal epithelium can unexpectedly occur in a Myc-independent manner.
A Comparative Experiment in Distributed Load Balancing

The anticipated uptake of Cloud computing, built on the well-established research fields of web services, networks, utility computing, distributed computing and virtualisation, will bring many advantages in cost, flexibility and availability for service users. These benefits are expected to further drive the demand for cloud services, increasing both the cloud customer base and the scale of cloud installations. This has implications for many technical issues in such Service Oriented Architectures and Internet of Services (IoS) type applications; fault tolerance, high availability and scalability for examples. Central to these issues is the establishment of effective load balancing techniques. It is clear that the scale and complexity of these systems makes centralized individual assignment of jobs to specific servers infeasible; leading to the need for an effective distributed solution. This paper investigates three possible distributed solutions, which have been proposed for load balancing: An approach inspired by the foraging behaviour of the Honeybee, Biased Random Sampling and Active Clustering.
Role of Aromatic l‐Amino Acid Decarboxylase for Dopamine Replacement by Genetically Modified Fibroblasts in a Rat Model of Parkinson's Disease

Abstract: Investigations of gene therapy for Parkinson's disease have focused primarily on strategies that replace tyrosine hydroxylase. In the present study, the role of aromatic l‐amino acid decarboxylase in gene therapy with tyrosine hydroxylase was examined by adding the gene for aromatic l‐amino acid decarboxylase to our paradigm using primary fibroblasts transduced with both tyrosine hydroxylase and GTP cyclohydrolase I. We compared catecholamine synthesis in vitro in cultures of cells with tyrosine hydroxylase and aromatic l‐amino acid decarboxylase together versus cocultures of cells containing these enzymes separately. l‐DOPA and dopamine levels were higher in the cocultures that separated the enzymes. To determine the role of aromatic l‐amino acid decarboxylase in vivo, cells containing tyrosine hydroxylase and GTP cyclohydrolase I were grafted alone or in combination with cells containing aromatic l‐amino acid decarboxylase into the 6‐hydroxydopamine‐denervated rat striatum. Grafts containing aromatic l‐amino acid decarboxylase produced less l‐DOPA and dopamine as monitored by microdialysis. These findings indicate that not only is there sufficient aromatic l‐amino acid decarboxylase near striatal grafts producing l‐DOPA, but also the close proximity of the enzyme to tyrosine hydroxylase is detrimental for optimal dopamine production. This is most likely due to feedback inhibition of tyrosine hydroxylase by dopamine.