Miracle-dz/UniFAR-FTUs huggingface dataset:
FNR Is a Global Regulator of Virulence and Anaerobic Metabolism in Salmonella enterica Serovar Typhimurium (ATCC 14028s)

ABSTRACT Salmonella enterica serovar Typhimurium must successfully transition the broad fluctuations in oxygen concentrations encountered in the host. In Escherichia coli, FNR is one of the main regulatory proteins involved in O2 sensing. To assess the role of FNR in serovar Typhimurium, we constructed an isogenic fnr mutant in the virulent wild-type strain (ATCC 14028s) and compared their transcriptional profiles and pathogenicities in mice. Here, we report that, under anaerobic conditions, 311 genes (6.80% of the genome) are regulated directly or indirectly by FNR; of these, 87 genes (28%) are poorly characterized. Regulation by FNR in serovar Typhimurium is similar to, but distinct from, that in E. coli. Thus, genes/operons involved in aerobic metabolism, NO· detoxification, flagellar biosynthesis, motility, chemotaxis, and anaerobic carbon utilization are regulated by FNR in a fashion similar to that in E. coli. However, genes/operons existing in E. coli but regulated by FNR only in serovar Typhimurium include those coding for ethanolamine utilization, a universal stress protein, a ferritin-like protein, and a phosphotransacetylase. Interestingly, Salmonella-specific genes/operons regulated by FNR include numerous virulence genes within Salmonella pathogenicity island 1 (SPI-1), newly identified flagellar genes (mcpAC, cheV), and the virulence operon (srfABC). Furthermore, the role of FNR as a positive regulator of motility, flagellar biosynthesis, and pathogenesis was confirmed by showing that the mutant is nonmotile, lacks flagella, is attenuated in mice, and does not survive inside macrophages. The inability of the mutant to survive inside macrophages is likely due to its sensitivity to the reactive oxygen species generated by NADPH phagocyte oxidase.
A coherence improvement technique for coherent change detection in SAR interferometry

This paper presents the new method to improve the coherence between the synthetic aperture radar (SAR) images for coherent change detection (CCD) by removing the fringe rate which is determined by the terrain topography and the interferometric baseline. This method performs without the information on the terrain topography and the flight path measured by the instruments such as the inertial navigation system (INS). The proposed method can successfully reveal the car track that is unnoticeable on the airborne SAR amplitude images of the 10cm resolution.
Paroxysmal extreme pain disorder mutations within the D3/S4–S5 linker of Nav1.7 cause moderate destabilization of fast inactivation

Single‐point missense mutations in the peripheral neuronal voltage‐gated sodium channel Nav1.7 are implicated in the painful inherited neuropathy paroxysmal extreme pain disorder (PEPD). The Nav1.7 PEPD mutations are located in regions of the channel suggested to play important roles in fast inactivation. PEPD mutations in the putative inactivation gate have been reported to significantly impair fast inactivation, resulting in pronounced persistent currents. However, PEPD mutations in the S4–S5 linker of domain 3 (D3/S4–S5) had not been characterized and the roles of specific residues in this linker in channel gating are unclear. We functionally characterized two of the D3/S4–S5 PEPD mutations (V1298F and V1299F) and compared their effects on gating to an adjacent non‐PEPD mutation (V1300F) and the I1461T PEPD mutation, located in the putative inactivation gate. The primary effect of the V1298F and V1299F mutations is to shift the voltage dependence of fast inactivation by ∼20 mV in the depolarizing direction. We observed a similar effect with the PEPD mutation I1461T. Interestingly, while all three PEPD mutations increased persistent currents, the relative amplitudes (∼6% of peak) were much smaller than previously reported for the I1461T mutation. In contrast, the main effect of the V1300F mutation was a depolarizing shift in the voltage dependence of activation. These data demonstrate that (1) mutations within D3/S4–S5 affect inactivation of Nav1.7 in a residue‐specific manner and (2) disruption of the fast‐inactivated state by PEPD mutations can be more moderate than previously indicated, which has important implications for the pathophysiology of PEPD.
Correlation between the light scattering and the mitochondrial content of normal tissues and transplantable rodent tumors.

The development of noninvasive optical studies necessitates an understanding of the biological parameters which affect light propagation in soft tissues. In the present report, we have measured the optical properties of various normal (i.e., perfused liver, brain, skeletal muscle, white adipose tissue) and neoplastic rodent tissues (i.e., glioma, hepatoma, mammary adenocarcinoma) by using time-resolved spectroscopy. The contribution of the hemoglobin (+ myoglobin in the case of muscle) to the total light absorption at 780 nm has been determined. This contribution varies from about 25% (brain, skeletal muscle) to about 100% (white adipose tissue, 13762A mammary adenocarcinoma, 9L glioma). These results are explained by different blood volume fractions in the tissues and by the existence at 780 nm of other chromophores, such as the mitochondrial cytochrome oxidase. Secondly, the dependence of the light scattering of the tissue on both the cell and the mitochondrial content has been analyzed. The results indicate that there is no correlation between the light scattering and the DNA content, measured as an indicator of the cell number in the tissue. The scattering coefficient is proportional to both the succinate dehydrogenase activity and the mitochondrial protein content of the tissue, which are indicators of the mitochondria content of the tissue when based upon estimates of tissue wet weight.
Concern Over Weight and Dieting in Taiwanese Adolescents: Correlations of Gender, Age, Weight, and Multidimensional Characteristics

The aims of this study were to compare the levels of concern over weight and dieting (COWD) among adolescents with different body weight status, gender, and age, and to examine the associations of COWD with multidimensional characteristics. Nine thousand eighty-seven adolescents completed the questionnaires. The levels of COWD were compared among the groups with different body weight status, gender, and age. The correlates of COWD in gender- and age-specified groups were examined. The results indicated that the levels of COWD varied across the groups of adolescents with different body weight status, gender, and age. Being overweight or obese, depression, and low self-esteem were associated with high COWD in all gender- and age-specified groups. A variety of socio-demographic, personal, family, peer, and school characteristics were also associated with high COWD in adolescents with specified gender and age. Gender- and age-specified intervention programs targeting adolescents with the correlates of high COWD should be considered.
Revisiting RNA-directed DNA methylation

RNA-directed DNA methylation (RdDM) involves sequence-specific guiding of the de novo methylation machinery to complementary genomic DNA by RNA molecules. It is still elusive whether guide RNAs bind directly to DNA or to nascent transcripts produced from it. Even the nature of the guide RNAs is not elucidated. RNA interference (RNAi) studies provided a link between RNAi and RdDM indicating that small interfering RNAs (siRNAs) trigger and guide cytosine methylation. The “siRNA hypothesis” is generally accepted. However, recent data demonstrated that RdDM is not always associated with the accumulation of corresponding siRNAs. RdDM triggers may differ from guide RNAs and further studies are needed to clarify if guide RNAs are small or long RNAs, if they are single or double stranded and if they target DNA or nascent transcript.
Research on the financial risk prevention of the coal enterprise diversification

Diversification is a mode of operation which is widely used by the development of group companies. The reason is that diversification can play internal strength, access to synergistic effect of resources, and enable enterprises to the orbit of strengthen and expand. But in reality, many businesses will also diversified into the development of difficulty or even go bankrupt. In order to stay sustainable in business, enterprises must be integrate their actual conduct to management and control effectively. By analyzing the status of China's coal enterprises diversification and the financial risks faced, we propose some measures to guard against financial risks, and provide final support for the sustainable and healthy development of the coal enterprises.
A flexible RNS-based large polynomial multiplier for Fully Homomorphic Encryption

In the era of the cloud computing, homomorphic encryption allows remote data processing while preserving confidentiality. Its main drawback, however, is the huge complexity in terms of operand size and computation time, which makes hardware acceleration desirable in order to achieve acceptable performance. In this paper, we present a flexible modular polynomial multiplier implemented through a high-level synthesis flow. We show that flexibility does not come at a price, and the proposed solution is competitive against custom designs.
Designing and Using Carbon Management Systems to Promote Ecologically Responsible Behaviors

With the hope of mitigating the harmful impacts of climate change, many organizations are taking actions to reduce their carbon footprints. Carbon-reducing initiatives in organizations are varied: they range from green product innovations to encouraging behavioral changes by customers and employees. Green IS can play an important role in environmental sustainability by supporting a number of these strategies. Drawing on theories of persuasive systems design, this paper explores how one category of Green IS, carbon management systems (CMS), can be designed and used in order to persuade employees to perform ecologically responsible behaviors. The results from three organizational case studies suggest that CMS can be effective at changing employees’ environmental behaviors, demonstrate the extent to which persuasive system design principles (including an emergent category of Integration) are reflected in CMS, and highlight the importance of understanding the persuasion context. The findings of the study are used to inform the development of four propositions, which can serve as a foundation for further research in the Green IS domain.
Effect of Perilla frutescens aqueous extract on free radical production by human neutrophil leukocytes.

OBJECTIVE The present study was intended to evaluate the antioxidant properties of aqueous extract of the Perilla frutescens (L.) Britton. MATERIAL AND METHODS The antioxidant properties of Perilla frutescens were analyzed employing neutrophil leukocytes stimulated by the nonopsonized Escherichia coli. The neutrophil leukocytes were affected by adding an aqueous extract of Perilla. The generation of the reactive oxygen species by neutrophil leukocytes was investigated using assessment of luminol- and lucigenin-dependent chemiluminescence. RESULTS We found out that the treatment of neutrophil leukocytes with the Perilla aqueous extract inhibited the release of reactive oxygen species, measured as luminol- and lucigenin-dependent chemiluminescence, by about 30% and more than 90%, respectively. CONCLUSION The results of this study show that the aqueous extract of the Perilla frutescens inhibits significantly free radical production by neutrophil leukocytes, which was especially obvious when the lucigenin-dependent chemiluminescence assessment method was applied.
Landscape of Somatic Retrotransposition in Human Cancers

Movement in the Cancer Genome Transposable elements are genetic sequences that can replicate and move within the genome. The factors that make an element mobile are unknown but are generally considered rare in mammals. Lee et al. (p. 967, published online 28 June) analyzed five cancer types occurring among several individuals and found that three types of epithelial tumors exhibited high rates of element movement relative to brain and blood cancers. Furthermore, these somatically acquired, tumor-specific elements targeted genes in colorectal cancer that, when disrupted, impact gene expression and thus may be a factor in the progression of the cancers. Whole-genome sequencing provides evidence for somatic insertions in colorectal, prostate, and ovarian cancers. Transposable elements (TEs) are abundant in the human genome, and some are capable of generating new insertions through RNA intermediates. In cancer, the disruption of cellular mechanisms that normally suppress TE activity may facilitate mutagenic retrotranspositions. We performed single-nucleotide resolution analysis of TE insertions in 43 high-coverage whole-genome sequencing data sets from five cancer types. We identified 194 high-confidence somatic TE insertions, as well as thousands of polymorphic TE insertions in matched normal genomes. Somatic insertions were present in epithelial tumors but not in blood or brain cancers. Somatic L1 insertions tend to occur in genes that are commonly mutated in cancer, disrupt the expression of the target genes, and are biased toward regions of cancer-specific DNA hypomethylation, highlighting their potential impact in tumorigenesis.
Lung Gene Expression Changes in Streptozotocin-induced Diabetic Rats

Background: Diabetes profoundly affects gene expression in organs such as heart, skele tal muscle, kidney and liver, with areas of perturbation including carbohydrate and lipid met abolism, oxidative stress, and protein ubiquitination. Type 1 diabetes impairs lung function, but whether gene exp ression alterations in the lung parallel those of other tissue types is lar gely unexplored. Methods: Lung from a rat model of diabetes mellitus induced by streptozotocin was subje cted to gene expression microarray analysis. Results: Glucose levels were 67 and 260 mg/dl (P<0.001) in control and diabetic rats (n =5, 7), respectively. There were 46 genes with at least ± 1.5-fold significantl y ltered expression (19 increases, 27 decreases). Gene ontology groups with significant over-representation am ong genes with altered expression included apoptosis (p=0.03, n=5 genes), response to stress (p=0.03, n=5), re gulation of protein kinase activity (p=0.04, n=4), ion transporter activity (p=0.01, n=8) and collagen ( p=0.01, n=3). All genes assigned to the apoptosis and response to stress groups had increas ed expre sion whereas all genes assigned to the collagen group had decreased expression. In contrast, the pro ein kinase activity and ion transporter activity groups had genes with both increased and decreased expr ession. Conclusions: Gene expression in the lung is affected by type 1 diabetes in several spec ific ar as, including apoptosis. However, the lung is resistant to changes in gene express ion lated to lipid and carbohydrate metabolism and oxidative stress that occur in other tissue types such as heart, skeletal muscle and kidney.
Health‐related quality of life in chronic coagulation disorders

Summary. Measurement of health‐related quality of life (HR‐QoL) is used in patients with haemophilia as a way of assessing the effectiveness of health care, especially as cure is not possible. We report the first such study on patients with chronic coagulation disorders in Australia, using The RAND 36‐item Health Survey 1.0 (SF‐36), a standardized validated questionnaire combined with a semistructured interview. The mean scores for the eight domains of the SF‐36 ranged from 52.5 ± 42.1 for physical role to 80.0 ± 20.0 for social functioning. Comparison with normative data obtained from the Australian Bureau of Statistics (ABS) demonstrated a reduction in all domains in this population with statistically significant reductions in general health, physical role limitation and vitality. Comparison with other studies indicates that the HR‐QoL of patients with haemophilia and von Willebrand's disorder in Australia is comparable with other Western countries, reflecting the overall similar quality of care available to these patients. This study also provides a good cross‐sectional view of the psychosocial factors of life in patients in Australia and recognizes the positive family support available to this population, while raising relevant shortcomings in schools and at the workplace that need to be studied further in a controlled manner.
Thymidine incorporation by lactating mammary epithelium during compensatory mammary growth in beef cattle.

Ten Hereford cows, 100 d into first lactation, were assigned to treatment or control groups to study compensatory growth of mammary glands. The right udder half of treatment cows was covered to prevent suckling by the calf, whereas control cows were suckled on all quarters. Milk production was estimated the day treatment began and 4 d later by machine milking following removal of calves for 12 h and i.v. injection of oxytocin. Five to 7 d after beginning treatment, cows were killed and mammary tissue was obtained from three regions within left and right glands for in vitro incubation with [3H]thymidine. Deoxyribonucleic acid of lactating udder halves did not increase in response to treatment although RNA: DNA ratio and milk production tended to increase. Incorporation of [3H]thymidine was greater in lactating quarters of treated cows than control cows (35,000 vs. 19,000 cpm/mg of DNA) with greatest incorporation in the basal regions of each gland. Furthermore, greatest incorporation of [3H]thymidine occurred in non-suckled glands. Autoradiographic analyses confirmed incorporation data and indicated that 81% of proliferating cells were epithelial. Data suggest that proliferation of mammary epithelial cells, within both the lactating and nonlactating glands, occurred in response to milk stasis.
Prevalence and risk factors of STDs in rural Haiti: implications for policy and programming in resource-poor settings

The goals of the current study are to: (1) estimate the prevalence of sexually transmitted diseases (STDs) among women accessing services at a women's health clinic in rural Haiti; and (2) identify risk factors for STDs in this setting. The design is a case control study, comparing risk factors for women who demonstrated positive laboratory results for chlamydia and/or gonorrhoea to women who tested negative for both of these pathogens. The strongest risk factors for chlamydia and/or gonorrhoea were largely economic variables, with work as a domestic servant increasing the risk by four-fold. Working as a market vendor reduced a woman's risk of having an STD by approximately 45%. Given that economic factors are strongly associated with STD risk in this context, one potential mechanism for reducing the risk of STDs, including HIV, would involve increasing economic opportunities for women in rural Haiti.
The influence of age and sex on the prevalence of depressive conditions: report from the National Survey of Psychiatric Morbidity

Background. Women are consistently reported to have a greater prevalence of depressive disorders than men. The reason for this is unclear, and is as likely to be social as biological. There is some evidence that the excess of depression is greater during women's reproductive lives. Data from the National Survey of Psychiatric Morbidity were used to test the hypothesis that the excess disappeared in the post-menopausal years and that obvious social explanations for this were inadequate. Method. Subjects (N=9792) from a random sample of the British population provided data for the analysis. Psychiatric assessment was carried out by lay interviewers using the CIS-R. Subjects with ICD-10 depressive episode or mixed anxiety/depression were compared with the remainder. Social variables that were likely to contribute to a post-menopausal decline in depressive disorders were controlled in logistic regression analyses. Results. There was a clear reversal of the sex difference in prevalence of depression in those over age 55. This could not be explained in terms of differential effects of marital status, child care, or employment status. Conclusions. This large and representative survey adds considerably to the increasingly held view that the sex difference in prevalence of depression is less apparent in later middle age. This may be linked to the menopause, and our attempts to explain it in terms of obvious conditions among social variables were not successful. More specific studies are required to clarify the finding.
Two-body decays of neutralinos and charginos.

We give explicit formulas for the two-body decays of the neutralinos and charginos of the minimal model of supersymmetry. There are two possible classes of two-body final states: (i) neutralino or chargino plus a W, Z, or Higgs boson; and (ii) channels involving squarks or sleptons. The important features of these decays are illustrated and their phenomenological implications discussed. The two-body decay into the lightest Higgs boson is almost always present, and enhances the heavy-quark component of the final state. In addition, two-body-decay branching ratios into a W or Z can be large for the heaviest charginos and neutralinos.
Predictive value of CA 125 and CA 72-4 in ovarian borderline tumors

Abstract Background: The aim of this study was to assess the prognostic value of cancer antigen (CA) 125 and CA 72-4 in patients with ovarian borderline tumor (BOT). Methods: All women diagnosed and treated for BOT at our institution between 1981 and 2008 were included into this retrospective study (n=101). Preoperatively collected serum samples were analyzed for CA 125 (Architect, Abbott and Elecsys, Roche) and CA 72-4 (Elecsys, Roche) with reference to clinical data and compared to healthy women (n=109) and ovarian cancer patients (n=130). Results: With a median of 34.7 U/mL (range 18.1–385.0 U/mL) for CA 125 and 2.3 U/mL (range 0.2–277.0 U/mL) for CA 72-4, serum tumor markers in BOT patients were significantly elevated as compared to healthy women with a median CA 125 of 13.5 U/mL (range 4.0–49.7 U/mL) and median CA 72-4 of 0.8 U/mL (range 0.2–20.6 U/mL). In addition, there was a significant difference compared with ovarian cancer patients who showed a median CA 125 of 401.5 U/mL (range 12.5–35,813 U/mL), but no difference was observed for CA 72-4 (median 3.9 U/mL, range 0.3–10,068 U/mL). Patients with a pT1a tumor stage had significantly lower values of CA 125 but not of CA 72-4 compared with individuals with higher tumor stages (median CA 125 29.9 U/mL for pT1a vs. 50.9 U/mL for >pT1a; p=0.014). There was a trend for increased concentrations of CA 125 but not of CA 72-4 in the presence of ascites, endometriosis or peritoneal implants at primary diagnosis. With respect to the prognostic value of CA 125 or CA 72-4, CA 125 was significantly higher at primary diagnosis in patients who later developed recurrence (251.0 U/mL vs. 34.65 U/mL, p=0.012). Conclusions: Serum CA 125 and CA 72-4 concentrations in BOT patients differ from healthy controls and patients with ovarian cancer. CA 125, but not CA 72-4, at primary diagnosis correlates with tumor stage and tends to be increased in the presence of ascites, endometriosis or peritoneal implants. Moreover, CA 125 at primary diagnosis appears to have prognostic value for recurrence. Clin Chem Lab Med 2009;47:537–42.