Miracle-dz/UniFAR-FTUs huggingface dataset:
V490M, a Common Mutation in 3-Phosphoglycerate Dehydrogenase Deficiency, Causes Enzyme Deficiency by Decreasing the Yield of Mature Enzyme*

A deficiency of 3-phosphoglycerate dehydrogenase (PHGDH) is a disorder of serine biosynthesis identified in children with congenital microcephaly, seizures, and severe psychomotor retardation. We report here the identification of the 1468G→A (V490M) mutation of this gene in two siblings of an Ashkenazi Jewish family, providing further evidence that the V490M mutation is a common, panethnic cause of this deficiency. Using a novel, DNA-based diagnostic test, the mutation was not detected in 400 non-Jewish controls; one heterozygote was found among 400 persons of Ashkenazi Jewish ethnicity. Extensive biochemical studies were undertaken to characterize the effect of this mutation on enzyme activity, turnover, and stability. The V490M PHGDH yielded less than 35% of the activity observed for the wild-type enzyme when overexpressed by transient transfection or when comparing the endogenous activity in fibroblast cells from the patients with controls. Immunoblotting studies showed a comparable reduction in the level of immunoreactive PHGDH in cells expressing the mutant enzyme. Pulse-chase experiments with metabolically labeled PHGDH indicated that this resulted from an increased rate of degradation of the mutant enzyme following its synthesis. Thermolability analyses of mutant and wild-type enzyme activity revealed no significant differences. While others have proposed that the V490M mutation decreases the V max of the enzyme, we conclude that this mutation impairs the folding and/or assembly of PHGDH but has minimal effects on the activity or stability of that portion of the V490M mutant that reaches a mature conformation.
Prediction of antidepressant effects of sleep deprivation by metabolic rates in the ventral anterior cingulate and medial prefrontal cortex.

OBJECTIVE Sleep deprivation has been shown to have an antidepressant benefit in a subgroup of depressed patients. Functional imaging studies by the authors and others have suggested that patients with elevated metabolic rates in the anterior cingulate gyrus at baseline are more likely to respond to either sleep deprivation or antidepressant medications than patients with normal metabolic rates. The authors extend their earlier work in a larger group of patients and explore additional brain areas with statistical probability mapping. METHOD Thirty-six patients with unipolar depression and 26 normal volunteers were studied with positron emission tomography before and after sleep deprivation. Response to sleep deprivation was defined as a 40% or larger decrease in total scores on the Hamilton Depression Rating Scale. RESULTS One-third of the depressed patients had a significant response to sleep deprivation. Responders had higher relative metabolic rates in the medial prefrontal cortex, ventral anterior cingulate, and posterior subcallosal gyrus at baseline than depressed patients who did not respond to sleep deprivation and normal volunteers. Lower Hamilton depression scores correlated significantly with lower metabolic rates in the left medial prefrontal cortex. After sleep deprivation, significant decreases in metabolic rates occurred in the medial prefrontal cortex and frontal pole in the patients who responded positively to sleep deprivation. CONCLUSIONS High pretreatment metabolic rates and decreases in metabolic rates after treatment in the medial prefrontal cortex may characterize a subgroup of depressed patients who improve following sleep deprivation and, perhaps, other antidepressant treatments.
Association between Polycystic Ovary Syndrome, Oral Microbiota and Systemic Antibody Responses

Polycystic ovary syndrome (PCOS) is a hormonal disorder of women that not only is the leading cause of infertility but also shows a reciprocal link with oral health. This study aimed to investigate the hypothesis that the levels of putative periodontal pathogens in saliva and their antibody response in serum are elevated in PCOS, compared to systemic health. A total of 125 women were included in four groups; 45 women with PCOS and healthy periodontium, 35 women with PCOS and gingivitis, 25 systemically and periodontally healthy women, 20 systemically healthy women with gingivitis. Salivary levels of seven putative periodontal pathogens were analyzed by quantitative real-time polymerase chain reaction and serum antibody levels were analyzed by ELISA. In women with PCOS, salivary Porphyromonas gingivalis, Fusobacterium nucleatum, Streptococcus oralis and Tannerella forsythia levels were higher than matched systemically healthy women, particularly in the case of gingivitis. Aggregatibacter actinomycetemcomitans and Treponema denticola levels were similar among study groups. The presence of PCOS also enhanced P. gingivalis, Prevotella intermedia and S. oralis serum antibody levels, when gingivitis was also present. Gingival inflammation correlated positively with levels of the studied taxa in saliva, particularly in PCOS. The presence of P. gingivalis and F. nucleatum in saliva also exhibited a strong positive correlation with the corresponding serum antibody levels. In conclusion, as an underlying systemic endocrine condition, PCOS may quantitatively affect the composition of oral microbiota and the raised systemic response to selective members of this microbial community, exerting a confounding role in resultant gingival inflammation and periodontal health. The most consistent effect appeared to be exerted on P. gingivalis.
Serious Games for Mental Health: Are They Accessible, Feasible, and Effective? A Systematic Review and Meta-analysis

Introduction The development and use of serious games for mental health disorders are on the rise. Yet, little is known about the impact of these games on clinical mental health symptoms. We conducted a systematic review and meta-analysis of randomized controlled trials that evaluated the effectiveness of serious games on symptoms of mental disorder. Method We conducted a systematic search in the PubMed, PsycINFO, and Embase databases, using mental health and serious games-related keywords. Ten studies met the inclusion criteria and were included in the review, and nine studies were included in the meta-analysis. Results All of the serious games were provided via personal computer, mostly on CD-ROM without the need for an internet connection. The studies targeted age groups ranging from 7 to 80 years old. The serious games focused on symptoms of depression (n = 2), post-traumatic stress disorder (n = 2), autism spectrum disorder (n = 2), attention deficit hyperactivity disorder (n = 1), cognitive functioning (n = 2), and alcohol use disorder (n = 1). The studies used goal-oriented (n = 4) and cognitive training games (n = 6). A total of 674 participants were included in the meta-analysis (380 in experimental and 294 in control groups). A meta-analysis of 9 studies comprising 10 comparisons, using a random effects model, showed a moderate effect on improvement of symptoms [g = 0.55 (95% confidence interval 0.28–0.83); P < 0.001], favoring serious games over no intervention controls. Discussion/conclusion Though the number of comparisons in the meta-analysis was small, these findings suggest that serious gaming interventions may be effective for reducing disorder-related symptoms. More studies are needed in order to attain deeper knowledge of the efficacy for specific mental disorders and the longer term effects of this new type of treatment for mental disorders.
A Simple and Compact Planar Ultra Wideband Antenna with Single or Dual Band-Notched Characteristics

A printed monopole ultra wideband (UWB) antenna with frequency band-notched characteristics is proposed and investigated. The antenna consists of a half-disk shaped structure combined with an inverted isosceles trapezoid structure. To achieve the frequency band notched characteristics, an open-ended thin slit with a length of about one quarter guided wavelength is inserted on the radiator. Multiple slits can be employed to realize multiple frequency band notched characteristics. To validate the concept, two prototypes aredesigned, fabricated and tested. The ¯rst is a single band notched UWB antenna whereas the second is a dual band notched UWB antenna. The simulated and measured results of both antennas are presented shown a reasonable agreement between them. The results also con¯rm the proposed UWB antenna design can achieve superior dual band-notch performance at desired frequency bands. 1
The concentration of 12-lipoxygenase in platelet rich plasma as an indication of cancer of the prostate

Aim of the study The aim of this study was to determine whether measuring concentrations of 12-LOX in platelet-rich plasma patients can: Differentiate between the group of patients with prostate cancer and healthy men. Correlate the degree of severity of the disease and the concentration of the enzyme. Material and methods The study group comprised 88 men (40–88 years), including 54 patients diagnosed with prostate cancer. The population was divided into 4 groups: group 1 (22 men, aged 55–84 years) –with a negative biopsy, group 2 (36 men, aged 54–88 years) – with a positive biopsy result, group 3 (18 participants aged 58–83) – patients with cancer metastatic disease, group 4 of healthy men (12 people aged 40–66 years) – biopsy was not performed. Routine PSA, morphology and CRP analysis were performed and platelet rich plasma was used for 12(S)LOX determination using an ELISA kit. Results There was a weak (r = 0.0487) positive correlation between the number of blood platelets and plasma 12(S)LOX. An inverse relationship between 12(S)LOX and Gleason grade was found. Heterogeneity of 12(S)LOX in the group with prostate cancer metastatic disease may suggest differences in the response to the treatment carried out. There were no statistically significant differences in concentrations of 12(S)LOX in different groups of patients. Conclusions Our results suggest that 12(S)LOX is relevant in prostate cancer; however, further study should include a larger, more select group of men with prostate cancer.
QCMUQ@QALB-2015 Shared Task: Combining Character level MT and Error-tolerant Finite-State Recognition for Arabic Spelling Correction

We describe the CMU-Q and QCRI’s joint efforts in building a spelling correction system for Arabic in the QALB 2015 Shared Task. Our system is based on a hybrid pipeline that combines rule-based linguistic techniques with statistical meth-ods using language modeling and machine translation, as well as an error-tolerant ﬁnite-state automata method. We trained and tested our spelling corrector using the dataset provided by the shared task orga-nizers. Our system outperforms the base-line system and yeilds better correction quality with an F-score of 68.12 on L1-test-2015 testset and 38.90 on the L2-test-2015. This ranks us 2nd in the L2 subtask and 5th in the L1 subtask.
An association between the estimated glomerular filtration rate and carotid atherosclerosis.

OBJECTIVE Chronic kidney disease (CKD) is a major public health problem. There is conflicting evidence concerning whether CKD is an independent risk factor for carotid intima-media thickness (IMT). PATIENTS AND METHODS The study subjects were 428 men aged 70+/-15 (mean+/-standard deviation) years and 582 women aged 75+/-12 years enrolled consecutively from patients in the Medical Department of Seiyo Municipal Nomura Hospital. Carotid IMT was derived via B-mode ultrasonography and CKD was evaluated by the estimated glomerular filtration rate (eGFR) using the Modification of Diet in Renal Disease Study equation. RESULTS In men, age (p<0.001), systolic blood pressure (p<0.001), antihypertensive drug use (p<0.001), HDL-C (p=0.006), LDL-C (p=0.004), prevalence of diabetes (p=0.035) and eGFR (p<0.001) were significantly correlated with carotid IMT. In women, age (p<0.001), systolic blood pressure (p<0.001), antihypertensive drug use (p<0.001), HDL-C (p=0.035), LDL-C (p=0.017) and eGFR (p<0.001) were significantly correlated with carotid IMT. Stepwise multiple linear regression analysis using IMT as an objective variable, adjusted by various factors as explanatory variables, showed that eGFR was a significant independent contributing factor along with known risk factors in men (beta, -0.096; p=0.018) and women (beta, -0.080; p=0.035). CONCLUSIONS Our data suggested that eGFR was associated with an increased prevalence of carotid atherosclerosis independent of common cardiovascular risk factors in both men and women.
Perinatal correlates and neonatal outcomes of small for gestational age infants born at term gestation.

OBJECTIVE We sought to examine the current perinatal correlates and neonatal morbidity associated with intrauterine growth failure among neonates born at term gestation. STUDY DESIGN We compared 372 small for gestational age (SGA, birth weight <10th percentile) infants born at term gestation to 372 appropriate for gestational age controls (AGA, birth weight 10th to 90th percentile) matched by sex, race, and gestational age within 2 weeks. RESULTS Compared with AGA controls, significant (P < .05) maternal risk factors for SGA status included single marital status (59% versus 53%), lower prepregnancy weight (144 +/- 41 lbs versus 153 +/- 40 lbs), lower weight gain during pregnancy (29 +/- 15 lbs versus 33 +/- 15 lbs), smoking (25% versus 17%), hypertension (14% versus 7%), and multiple gestation (9% versus 2%). Mothers of SGA infants were more likely to undergo multiple (>or=3) antenatal ultrasound evaluations (19% versus 7%), biophysical profile monitoring (11% versus 4%), and oxytocin delivery induction (28% versus 16%) (P < .05). Pediatrician attendance was more common among SGA deliveries (50% versus 37%, P < .05). SGA infants had significantly higher rates of hypothermia (18% versus 6%) and symptomatic hypoglycemia (5% versus 1%). These neonatal problems remained significant even when medical or pathologic causes of intrauterine growth failure, including pregnancy hypertension, multiple gestation, and congenital malformations, were excluded. CONCLUSION Despite higher rates of pregnancy complications among mothers of SGA infants, the rates of neonatal adverse outcomes are low. However, SGA infants remain at risk for hypothermia and hypoglycemia and require careful neonatal surveillance.
Investigating dispersion and nonlinearity interaction in optical fibers for hybrid optical telecommunication systems

The effect of interaction between fiber dispersion and nonlinearities in DWDM hybrid optical communication system is investigated. Eight DWDM wavelengths, 100-GHz spaced chosen on ITU-grid were used in the study. Different hybrid configurations of 10 Gbps and 40 Gbps signals were considered. Numerical simulations were conducted to predict the performance of each signal transmitted. Bit-error-rate criterion was used to quantify the performance of each signal. Optimal regimes of operation were found for different hybrid configurations.
An Integrated Framework forAnalysing Changing Requirements

The problem of analysing the eeects of changing requirements imposes strict demands on system representations, particularly in safety-critical domains. We argue that solving this problem will require structured representations that highlight the interaction between requirements, and record the rationale for decisions made during the development process. As a means of providing and analysing this information, we propose a framework, called goal-structured analysis, that integrates three components: a goal-oriented model for imposing the desired structure on requirements, natural language processing for useability of the system and avoidance of change via the creation of clear speciications, and formal reasoning for performing impact and sensitivity analaysis.
Software testing - the state of the practice

The main factor preventing delivery of high quality software systems is the difficulty of finding and eliminating latent software defects. Software errors - very much like "design faults" in pure hardware lbased systems - often reveal themselves in very unpleasant and unexpected ways. Systematic software testing is the best defense against such software quality problems. The intricacies and complexity of non-trivial software products i n practice dictate some form of automated software testing. A software product in the 10 KLOC to 50 KLOC range may have billions of internal states, tens of thousands of variables, and thousands of different "functional behaviors" or "features. " Analyzing such a system manually - while an interesting application of modern Computer Science - isn¿t much fun, and doesn¿t often produce much defect detection benefit.
MEKA: A Multi-label/Multi-target Extension to WEKA

Multi-label classification has rapidly attracted interest in the machine learning literature, and there are now a large number and considerable variety of methods for this type of learning. We present MEKA: an open-source Java framework based on the well-known WEKA library. MEKA provides interfaces to facilitate practical application, and a wealth of multi-label classifiers, evaluation metrics, and tools for multi-label experiments and development. It supports multi-label and multi-target data, including in incremental and semi-supervised contexts.
Oat Protects against Diabetic Nephropathy in Rats via Attenuating Advanced Glycation End Products and Nuclear Factor Kappa B

Oat, a rich source of soluble fiber, was considered to have a possible preventive effect on the progression of diabetic nephropathy. The present study aimed to assess this preventive activity in a rat model of diabetic nephropathy. Adult Wister rats were injected by streptozotocin (65 mg/kg). Animals were fed with normal diet or with a diet containing 20% oat (W/W) for 21 weeks. At the end of 21 weeks, all the kidney tissues were collected for various examinations. Our results suggested that oat could decrease the Scr and glucose level in blood of diabetic rats significantly (P < 0.05), and increase the creatinine clearance (P < 0.01). In histopathological examination, oat-fed rats showed a significant decrease in glomerulus segmented sclerosis and incidence of tubule vacuolar degeneration. By ELISA, we reported that oat feeding resulted in decreasing the levels of IL-6 and AGE in serum and kidney homogenate. In addition, the levels of oxidative stress markers were markedly improved as a result of oat feeding. Furthermore, using EMSA, we showed that oat attenuated the activation of NF-κB. Using RT-PCR, we found that oat could downregulate the TGF-β1 and RAGE expression at mRNA levels. This study suggests that oat can suppress diabetic nephropathy in rats effectively and may slow down the renal fibrosis by the disruption of the detrimental AGE-RAGE-NFκB axis.
A Passive Self-Configuration MAC Protocol for IEEE 802.11-Based Multi-Hop MANETs

The paper proposes a passive self-configuration MAC protocol (PSC-MAC) for IEEE 802.11-based multi-hop MANETs. PSC-MAC focuses on determining multiple supervising sets, each of which consists of some power-rich stations, supervisors, to be in charge of the network management. Supervisor determination in PSC-MAC is achieved by a passive manner due to less communication overhead. The main idea of PSC-MAC is beacon interleaving, which guarantees that supervisors in different supervising sets transmit beacons in the different beacon intervals. The proposed rules, deficiency, isolation, and partition rules, enable each station to dynamically and passively transit its role to either a supervisor or a member. Simulation results show that PSC-MAC outperforms IEEE 802.11 and the previous research in terms of supervisor determination, clock synchronization, and energy efficiency
Discovery of optical emission from the supernova remnant G 32.8 0.1 (Kes 78)

Deep optical CCD images of the supernova remnant G 32.8−0.1 were obtained where filamentary and diffuse emission was discovered. The images were acquired in the emission lines of Hα + [N ii ]a nd [Sii]. Filamentary and diffuse structures are detected in most areas of the remnant, while no significant [O iii] emission is present. The flux-calibrated images suggest that the optical emission originates from shock-heated gas since the [S ii]/Hα ratio is greater than 1.2. The Spitzer images at 8 μm and 24 μm show a few filamentary structures to be correlated with the optical filaments, while the radio emission at 1.4 GHz in the same area is found to be very well correlated with the brightest optical filaments. The results from deep long-slit spectra also support the origin of the emission being from shock-heated gas ([S ii]/H α> 1.5). The absence of [O iii] emission indicates slow shock velocities into the interstellar “clouds” (≤100 km s −1 ), while the [S ii]λλ 6716/6731 ratio indicates electron densities up to ∼200 cm −3 . T he Hα emission is measured to lie between 1.8 to 4.6 × 10 −17 erg s −1 cm −2 arcsec −2 , while from VGPS Hi images the distance to the SNR is estimated to be between 6 to 8.5 kpc.
Does the use of passive or active consent affect consent or completion rates, or dietary data quality? Repeat cross-sectional survey among school children aged 11–12 years

Objectives An expectation of research is that participants should give fully informed consent. However, there is also a need to maximise recruitment to ensure representativeness. We explored the impact of passive or active parental consent on consent, completion rates and on dietary data quality in a survey among children aged 11–12 years. Setting Six middle schools in North-East England. Participants All children aged 11–12 years attending the six middle schools were eligible to participate (n=1141). Main outcomes Primary outcomes: whether or not each eligible child's parent gave consent and provided a complete dietary diary; whether or not a child completed their dietary diary but only among children who agreed to participate, and whether or not children providing diaries were classified as an under-reporter or not. Results Parents were more likely to consent passively than actively. This difference was greater among the more deprived: OR 16.9 (95% CI 5.7 to 50.2) in the least and 129.6 (95% CI 39.9 to 420.6) in the most deprived quintile (test for interaction: method of consent by level of deprivation, p=0.02). For all children eligible, completion was more likely if passive consent was used (OR 2.8, 95% CI 2.2 to 3.7). When only children who gave consent are considered, completion was less likely when passive rather than active consent was used (OR 0.6, 95% CI 0.4 to 0.9). Completion rate decreased as level of deprivation increased; we found no evidence that the OR for the method of consent varied by level of deprivation. There was no evidence that the quality of dietary data, as measured by an assessment of under-reporting, differed by method of consent (OR 0.8, 95% CI 0.5 to 1.2). Conclusions Passive consent led to a higher participation rate and a more representative sample without compromising data quality.
Decline of the Space Density of Quasars between z = 2 and z = 4

We define a new complete sample of 13 optically luminous radio quasars [MAB(1450 Å) < -26.9 mag and log P1.4 GHz(W Hz-1) > 25.7] with redshift 3.8 < z < 4.5, obtained by cross-correlating the Faint Images of the Radio Sky at Twenty cm (FIRST) radio survey and the Automatic Plate Measuring Facility catalog of POSS I. We measure the space density to be 1.0 ± 0.3 Gpc-3, a factor of 1.9 ± 0.7 smaller than the space density of similar quasars at z ≈ 2 (FIRST Bright Quasar Survey). Using a new measurement of the radio-loud fraction of quasars, we find that at z = 4 the total space density of quasars with MAB(1450 Å) < -26.9 mag is 7.4 ± 2.6 Gpc-3. This is a factor of 1.8 ± 0.8 less than the space density at z ≈ 2, found by the Two-Degree Field quasar survey. This z = 2/z = 4 ratio, consistent with that of the radio-loud quasars, is significantly different from the ratio of ~10 found for samples including lower luminosity quasars. This suggests that the decline of the space density beyond z ≈ 2 is slower for optically luminous quasars than for less luminous ones.