Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational Analysis of Deinococcus radiodurans Bacteriophytochrome Reveals Key Amino Acids Necessary for the Photochromicity and Proton Exchange Cycle of Phytochromes*

The ability of phytochromes (Phy) to act as photointerconvertible light switches in plants and microorganisms depends on key interactions between the bilin chromophore and the apoprotein that promote bilin attachment and photointerconversion between the spectrally distinct red light-absorbing Pr conformer and far red light-absorbing Pfr conformer. Using structurally guided site-directed mutagenesis combined with several spectroscopic methods, we examined the roles of conserved amino acids within the bilin-binding domain of Deinococcus radiodurans bacteriophytochrome with respect to chromophore ligation and Pr/Pfr photoconversion. Incorporation of biliverdin IXα (BV), its structure in the Pr state, and its ability to photoisomerize to the first photocycle intermediate are insensitive to most single mutations, implying that these properties are robust with respect to small structural/electrostatic alterations in the binding pocket. In contrast, photoconversion to Pfr is highly sensitive to the chromophore environment. Many of the variants form spectrally bleached Meta-type intermediates in red light that do not relax to Pfr. Particularly important are Asp-207 and His-260, which are invariant within the Phy superfamily and participate in a unique hydrogen bond matrix involving the A, B, and C pyrrole ring nitrogens of BV and their associated pyrrole water. Resonance Raman spectroscopy demonstrates that substitutions of these residues disrupt the Pr to Pfr protonation cycle of BV with the chromophore locked in a deprotonated Meta-Rc-like photoconversion intermediate after red light irradiation. Collectively, the data show that a number of contacts contribute to the unique photochromicity of Phy-type photoreceptors. These include residues that fix the bilin in the pocket, coordinate the pyrrole water, and possibly promote the proton exchange cycle during photoconversion.
Cyber attacks in cyber-physical power systems: A case study with GPRS-based SCADA systems

With the integration of computing, communication, and physical processes, the modern power grid is becoming a large and complex cyber physical power system (CPPS). This trend is intended to modernize and improve the efficiency of the power grid, yet it makes the CPPS vulnerable to potential cascading failures caused by cyber-attacks, e.g., the attacks that are originated by the cyber network of CPPS. To prevent these risks, it is essential to analyze how cyber-attacks can be conducted against the CPPS and how they can affect the power systems. In light of that General Packet Radio Service (GPRS) has been widely used in CPPS, this paper provides a case study by examining possible cyber-attacks against the cyber-physical power systems with GPRS-based SCADA system. We analyze the vulnerabilities of GPRS-based SCADA systems and focus on DoS attacks and message spoofing attacks. Furthermore, we show the consequence of these attacks against power systems by a simulation using the IEEE 9-node system, and the results show the validity of cascading failures propagated through the systems under our proposed attacks.
Drivers of measles mortality: the historic fatality burden of famine in Bangladesh

SUMMARY Measles is a major cause of childhood morbidity and mortality in many parts of the world. Estimates of the case-fatality rate (CFR) of measles have varied widely from place to place, as well as in the same location over time. Amongst populations that have experienced famine or armed conflict, measles CFR can be especially high, although past work has mostly focused on refugee populations. Here, we estimate measles CFR between 1970 and 1991 in a rural region of Bangladesh, which experienced civil war and famine in the 1970s. We use historical measles mortality data and a mechanistic model of measles transmission to estimate the CFR of measles. We first demonstrate the ability of this model to recover the CFR in the absence of incidence data, using simulated mortality data. Our method produces CFR estimates that correspond closely to independent estimates from surveillance data and we can capture both the magnitude and the change in CFR suggested by these previous estimates. We use this method to quantify the sharp increase in CFR that resulted in a large number of deaths during a measles outbreak in the region in 1976. Most of the children who died during this outbreak were born during a famine in 1974, or in the 2 years preceding the famine. Our results suggest that the period of turmoil during and after the 1971 war and the sustained effects of the famine, is likely to have contributed to the high fatality burden of the 1976 measles outbreak in Matlab.
Prevalence, risk factors and associations of primary Raynaud's phenomenon: systematic review and meta-analysis of observational studies

Objective To systematically review the literature with regard to the prevalence, incidence, risk factors and associations of primary Raynaud's phenomenon (PRP). Method A systematic review of the literature of observational studies for PRP was undertaken using five electronic databases. Any studies reporting prevalence, incidence and risk factors of PRP were collected. Relative risk or OR and 95% CI were extracted or calculated to present the association between risk factors and PRP. Random effects model was used to pool the results. Results 33 articles assessing a total of 33 733 participants were included in this analysis (2 cohort, 17 cross-sectional and 14 case–control studies). The pooled prevalence of PRP was 4.85% (95% CI 2.08% to 8.71%) in the general population. The pooled annual incidence of PRP was 0.25% (95% CI 0.19% to 0.32%). Risk factors and associations for PRP included female gender (OR=1.65, 95% CI 1.42 to 1.91), family history (OR=16.6, 95% CI 7.44 to 36.8), smoking (OR=1.27, 95% CI 1.06 to 1.53), manual occupation (OR=2.66 95% CI 1.73 to 4.08), migraine (OR=4.02, 95% CI 2.62 to 6.17), cardiovascular disease (OR=1.69, 95% CI 1.22 to 2.34) and marital status (married, OR=0.60, 95% CI 0.43 to 0.83). The definition of PRP varied considerably between studies. Conclusions This is the first systematic review of the prevalence, incidence, risk factors and associations of PRP. Further study using uniform strict criteria for the condition is required to confirm these findings, particularly the possible association with cardiovascular disease.
Comparison of High and Moderate Intensity of Strength Training on Mood and Anxiety in Older Adults

This study was designed to examine the psychological benefits of anaerobic exercise for older adults. Specifically, strength training was employed to examine the effects on mood and anxiety in a group of healthy but sedentary older women. 36 women (mean age = 68.5 yr.) were randomly assigned to groups given high intensity or moderate intensity strength training or to a control group. Strength training was conducted three days a week for 12 weeks. After the training period, both high and moderate strength-training programs produced marked improvements in muscle strength and body composition compared to the control subjects. The average improvements in the high and moderate intensity strength-training groups for muscle strength were 40.5 and 35.5%, respectively, and for percent body fat 1.52 and 2.50%, respectively. As for psychological changes, both training groups significantly improved positive mood (vigor), and the moderate intensity group significantly reduced trait anxiety compared to means of the control group. Also, both training groups showed some decrease in tension and state anxiety after the training period. These findings provide evidence for the effectiveness of anaerobic training to enhance perception of psychological well-being in older women. A moderate intensity rather than high intensity of training regimen may be more beneficial for sedentary older women to improve psychological health.
Early treatment with ganciclovir to prevent cytomegalovirus disease after allogeneic bone marrow transplantation.

BACKGROUND Cytomegalovirus (CMV) infection is a major cause of morbidity and mortality after allogeneic bone marrow transplantation. We conducted a controlled trial of ganciclovir for the early treatment of CMV infection in asymptomatic recipients of bone marrow transplants whose surveillance cultures for CMV became positive. METHODS Bone marrow--allograft recipients who were seropositive for CMV antibodies or who received seropositive marrow were screened for CMV excretion by culture of throat swabs, blood, urine, or bronchoalveolar-lavage fluid. In this double-blind trial, 72 patients who had marrow engraftment and were excreting virus were randomly assigned to receive either placebo or ganciclovir (5 mg per kilogram of body weight twice a day for one week, followed by 5 mg per kilogram per day) for the first 100 days after transplantation. Patients were followed for the development of biopsy-confirmed CMV disease, ganciclovir-related toxicity, and survival. RESULTS Between assignment to the study drug and day 100 after transplantation, CMV disease developed in only 1 of the 37 patients assigned to receive ganciclovir (3 percent), but in 15 of the 35 patients assigned to receive placebo (43 percent, P less than 0.00001). The ganciclovir recipients had rapid suppression of virus excretion; 85 percent had negative cultures after one week of treatment, as compared with 44 percent of the placebo group (P = 0.001). The principal toxic reaction was neutropenia; 11 ganciclovir recipients had an absolute neutrophil count below 0.75 x 10(9) per liter, as compared with 3 placebo recipients (P = 0.052). Treatment was discontinued in 11 ganciclovir recipients and 1 placebo recipient because of neutropenia (P = 0.003). After treatment was stopped, the neutrophil count recovered in all patients. Overall survival was significantly greater in the ganciclovir group than in the placebo group both 100 days and 180 days after transplantation (P = 0.041 and 0.027, respectively). CONCLUSIONS Early treatment with ganciclovir in patients with positive surveillance cultures reduces the incidence of CMV disease and improves survival after allogeneic bone marrow transplantation.
Effects of psychological empowerment on the performance of R&D employees: Moderating effects of LOC

To test the relationship between psychological empowerment and R&D employees' work performance (including task performance, contextual performance and innovation performance), and the moderating effect of Locus of Control, we collected paired data of 189 R&D employees and their supervisors from a large foreign-funded R&D institution in China. The results show that psychological empowerment has significant positive influence on R&D employees' task performance, contextual performance and innovation performance. In case of ‘internals,’ the impact of psychological empowerment on contextual and innovation performance is more significant than for ‘externals. ’ The article concludes with a discussion of the theoretical values of this study, and its implications for managements in practice.
Upregulated MiR-1269 in hepatocellular carcinoma and its clinical significance.

OBJECTIVES MicroRNAs (miRNAs) are small, non-coding RNAs that have been increasingly shown important roles in various classes of cancers. However, miR-1269 has not been comprehensively studied in hepatocellular carcinoma (HCC). Thus, the purpose of the study was to evaluate the relationship between the expression of miR-1269 and clinicopathological parameters in HCC patients, and to predict its potential target genes. METHODS Total RNA was extracted from 95 pairs of HCC and matching adjacent non-cancerous tissues. The level of miR-1269 expression was detected by using quantitative real-time RT-PCR and calculated with the 2(-ΔCq) method. Eighteen online biological databases were used for targets prediction. RESULTS MiR-1269 expression was up-regulated in HCC tissues (1.9264±0.7160) compared to their non-tumor livers (1.5518±0.7273, P < 0.001). Level of miR-1269 was positively correlated to tumor nodes (r = 0.206, P = 0.046), metastasis (r = 0.203, P = 0.049), portal vein tumor embolus (r = 0.247, P = 0.016), vaso-invasion (r = 0.273, P = 0.008), tumor capsular infiltration (r = 0.407, P < 0.001) and expression of MTDH (r = 0.211, P = 0.005). Finally, 7 databases could be applied for the target prediction successfully. There were 9 targeted genes which had been shown concurrently by at least 4 databases: AGAP1, AGK, BPTF, C16orf74, DACT1, LIX1L, RBMS3, ZNF706 and BMPER. CONCLUSIONS MiR-1269 may be possibly involved in the tumorigenesis and progress of HCC. MiR-1269 could also act as a potential biomarker for the prognosis prediction for HCC.
Dynamics of Mast Cells in Lymph Node Following Antigenic Stimulation

Dynamics of mast cells in rat cervical lymph nodes were examined using conventional histological techniques after injection of Salmonella paratyphi B‐H antigen. There was no significant change in the number of mast cells at sixth hour and on the first day of stimulation compared with the controls. The number of mast cells was increased in all lymph node compartments on the second day of stimulation, which continued in the following 3 days. On the eighth day of stimulation, although the mast cell number decreased in the subcapsular area, it was still high in the paracortical area and medullary sinuses of the lymph nodes. On the second day of stimulation, the mast cell number was apparently increased in the subcapsular area than those of the other compartments. In the following days of stimulation, the highest number of mast cells was seen in the medullary sinuses. The highest paracortical mast cell number was determined on the third day of stimulation and some mast cells were observed near the high endothelial venules (HEVs). The changes of mast cell number among the lymph node compartments after antigenic stimulation support the hypothesis that the migration of mast cells occurred. This migration pattern indicates that mast cells enter the lymph node via afferent lymphatics and migrate to the lymph node compartments following antigenic stimulation.
Staphylococcal Enterotoxin-B-Mediated Stimulation of Interleukin-13 Production as a Potential Aetiologic Factor in Eczema in Infants

Background: Staphylococcus aureus colonization has been found in 80–100% of lesional skin from patients with atopic eczema dermatitis syndrome (AEDS) and is thought to have a role in the pathogenesis of the disease. Furthermore, up to 65% of S. aureus from lesional skin has been shown to produce toxigenic superantigens. Methods: Using a cohort of 11 children under 2 years of age diagnosed with AEDS, we isolated peripheral blood mononuclear cells, cultured them with staphylococcal enterotoxin B (SEB) and phytohaemagglutinin, and assessed the cytokine response profiles. Plasma was also collected for immunoglobulin E analysis. In addition, skin and nasal swabs were taken and cultured to determine the presence of SEB-producing S. aureus by polymerase chain reaction (PCR) and reverse passive latex agglutination. Results: We found a significant increase in the production of the SEB-induced cytokines interleukin (IL)-5 and IL-13 in the patient group when compared with non-atopic, healthy controls. For IL-13, there was almost no overlap in the levels between the groups. However, there was no correlation between SEB-induced IL-13 and disease severity. This difference was not seen when heat-inactivated S. aureus was used to stimulate the cells. Conclusions: IL-13 is an important factor in AEDS development in early childhood, and prophylactic anti-staphylococcal treatment may provide protection from AEDS in atopic individuals.
The effects of phytase and root hydroalcoholic extract of Withania somnifera on productive performance and bone mineralisation of laying hens in the late phase of production

1. A 6-week study was conducted to investigate the effects of phytase and hydroalcoholic extract of Withania somnifera root (WS) on productive performance and bone mineralisation of laying hens in the late phase of production. 2. Diets were arranged factorially (3 × 2 × 2) and consisted of a positive control with adequate Ca (4·37%) and nonphytate P (NPP; 0·39%) and a negative control diet with Ca (4·06%) and NPP (0·36 %); three concentrations of Withania somnifera (0, 65 and 130 mg/kg diet); and two concentrations of microbial phytase (0 and 300 U/kg diet). 3. A total of 144 72-week-old Hy-Line W36 laying hens were randomly assigned to the 12 treatment groups. Each treatment was replicated 4 times (4 x 3 hens). Egg production and egg weight were recorded daily, while feed intake and egg quality traits were recorded every two weeks. Bone quality traits were evaluated at the end of experiment. 4. Withania somnifera supplementation increased egg production and lowered egg weight only in the second two weeks of the experiment. Addition of phytase significantly depressed specific gravity of the eggs for the entire experiment period. No dietary treatment effects were observed on egg shell thickness and yolk weight. 5. Withania somnifera at 130 mg/kg did not affect feed intake. The hens fed on the positive control diet had higher albumen weight than the negative control diet in the second two-week period. Supplementation of the positive control diet with 65 mg/kg Withania somnifera in the absence of phytase significantly improved shell weight compared with the negative control (5·779 vs. 5·273 g respectively). 6. Supplementing Withania somnifera significantly improved Ca and P retention in tibia bone. In addition, an increase in tibia bone P was observed with phytase supplementation. There were significant interactions between Withania somnifera content and phytase for tibia bone Ca and P. 7. The results of this experiment indicated that dietary Withania somnifera has beneficial effects on tibia bone Ca and P content, and phytase improved tibia bone P retention without adverse effects on productive performance.
In Vivo Insulin Action Is Familial Characteristic in Nondiabetic Pima Indians

Non-insulin-dependent diabetes mellitus (NIDDM) is a genetic disorder characterized by two major pathogenic processes: reduced insulin action and a relative or absolute decrease in plasma insulin concentrations. We studied 116 nondiabetic siblings from 45 families to determine if in vivo insulin action showed any aggregation among siblings. Subjects were Pima Indians from the Gila River Indian Community in Arizona who, as a group, have the highest reported incidence and prevalence of NIDDM in the world. In vivo insulin action was determined by the euglycemic-clamp technique at two rates of insulin infusion in each subject with resulting mean plasma insulin concentrations of 119 and 1938 μU/ml. After adjustment for age, sex, and degree of obesity, there was significant aggregation among siblings of in vivo insulin action at the high insulin infusion rate (P < .0001). Family membership independently accounted for ∼34% of the variance in this measure of insulin action. Glucose uptake at the lower insulin infusion rate also showed familial aggregation (P < .01), with family membership independently accounting for ∼15% of the variance of this measurement. We conclude that in vivo insulin action is a familial characteristic. The familial component of insulin action occurs in addition to the effects of obesity, age, and sex on insulin action. Therefore it is not sufficient to simply know that an individual is lean or obese to predict his/her in vivo insulin resistance, because it must also be known whether he/she is from an insulin-resistant or insulin-sensitive family. An alteration of insulin action may be an underlying and potentially genetically determined abnormality in Pima Indians that could help explain the familial aggregation of diabetes in this population. Such a genetic mechanism might also operate in populations with Native American admixture (e.g., Mexicans) as well as other populations.
Specific Antibodies to Porphyromonas gingivalisLys-Gingipain by DNA Vaccination Inhibit Bacterial Binding to Hemoglobin and Protect Mice from Infection

ABSTRACT Lys-gingipain (KGP), a lysine-specific cysteine proteinase, is one of the major virulence factors of Porphyromonas gingivalis. Here we examined the involvement of the catalytic domain of KGP (KGPcd) in hemoglobin binding by P. gingivalis, using a specific immunoglobulin G (IgG) elicited by the administration of plasmid DNA encoding KGPcd or the catalytic domain of Arg-gingipain (RGPcd). The pSeq2A/kgpcd and pSeq2B/rgpcd plasmids were constructed by the ligation of kgpcd andrgpcd DNA fragments, respectively. Female BALB/c mice were immunized with each of these plasmids. pSeq2A/kgpcd elicited a strong response to recombinant KGPcd (rKGPcd), as well as to comparably produced rRGPcd-reactive antibodies. The serum antibodies elicited by pSecTag2B/rgpcd also cross-reacted with rKGPcd as well as rRGPcd. Anti-KGPcd IgG significantly inhibited hemoglobin binding by P. gingivalis. Furthermore, the inhibition of hemoglobin binding was markedly enhanced by a combination of anti-KGPcd and anti-fimbriae. Anti-RGPcd IgG showed a negligible inhibitory effect, while both anti-KGPcd and anti-RGPcd IgGs showed significant inhibitory effects on Lys- and Arg-specific proteolytic activities and on the growth of P. gingivalis under iron-restricted conditions where supplemented hemoglobin was the sole iron source. Immunized mice were challenged by intraperitoneal inoculation with P. gingivalis. All nonimmunized mice died within 72 h; however, vaccination with pSeq2A/kgpcd and pSeq2B/rgpcd prevented inflammatory responses and prolonged the survival rate of immunized mice by 43 and 27%, respectively. These results suggest that KGPcd acts as a hemoglobin-binding protein and can also be useful as an immunogen inducing a protective response to P. gingivalis infection.
Evaluation on the selection of video quality metrics for overall visual perception

Multimedia quality assessment has become an important issue for both monitoring and control of multimedia networks and for the optimization of the new algorithms for audiovisual enhancement. In this paper we evaluate various objective video quality metrics in respect to their match to the subjective assessment represented as mean opinion score (MOS). The proposed framework is aimed for low bit-rate MPEG-2 sequences in SD and HD format. We consider 29 objective measures for no-reference video quality assessment and rank them according to their match to the MOS independently and based on the cross-correlation between the objective measures. The selected set of ranked measures are incorporated into the proposed neural network scheme for estimating the overall visual perception. The selection of measures is done using the proposed linear model which aims at maximizing measure correlation to MOS and at the same time minimizing mutual correlation between the selected set of measures. The proposed VQA model is intended for (i) estimation of the overall visual quality and (ii) the evaluation of the objective video quality metrics for particular applications defined by the test sequences and corresponding visual perception results. We present the results of the proposed method on SD and HD sequences for different number of selected measures and provide comparison results (to the state-of-the-art methods) of the overall estimated quality.