Miracle-dz/UniFAR-FTUs huggingface dataset:
Spectroscopic Studies of the Iron and Manganese Reconstituted Tyrosyl Radical in Bacillus Cereus Ribonucleotide Reductase R2 Protein

Ribonucleotide reductase (RNR) catalyzes the rate limiting step in DNA synthesis where ribonucleotides are reduced to the corresponding deoxyribonucleotides. Class Ib RNRs consist of two homodimeric subunits: R1E, which houses the active site; and R2F, which contains a metallo cofactor and a tyrosyl radical that initiates the ribonucleotide reduction reaction. We studied the R2F subunit of B. cereus reconstituted with iron or alternatively with manganese ions, then subsequently reacted with molecular oxygen to generate two tyrosyl-radicals. The two similar X-band EPR spectra did not change significantly over 4 to 50 K. From the 285 GHz EPR spectrum of the iron form, a g 1-value of 2.0090 for the tyrosyl radical was extracted. This g 1-value is similar to that observed in class Ia E. coli R2 and class Ib R2Fs with iron-oxygen cluster, suggesting the absence of hydrogen bond to the phenoxyl group. This was confirmed by resonance Raman spectroscopy, where the stretching vibration associated to the radical (C-O, ν7a = 1500 cm−1) was found to be insensitive to deuterium-oxide exchange. Additionally, the 18O-sensitive Fe-O-Fe symmetric stretching (483 cm−1) of the metallo-cofactor was also insensitive to deuterium-oxide exchange indicating no hydrogen bonding to the di-iron-oxygen cluster, and thus, different from mouse R2 with a hydrogen bonded cluster. The HF-EPR spectrum of the manganese reconstituted RNR R2F gave a g 1-value of ∼2.0094. The tyrosyl radical microwave power saturation behavior of the iron-oxygen cluster form was as observed in class Ia R2, with diamagnetic di-ferric cluster ground state, while the properties of the manganese reconstituted form indicated a magnetic ground state of the manganese-cluster. The recent activity measurements (Crona et al., (2011) J Biol Chem 286: 33053–33060) indicates that both the manganese and iron reconstituted RNR R2F could be functional. The manganese form might be very important, as it has 8 times higher activity.
Sex Differences in Sex Hormones, Carotid Atherosclerosis, and Stroke.

There are notable sex differences in cardiovascular disease. Although the cumulative incidence of cardiovascular disease in women lags behind that of men by ≈7 to 10 years, strokes comprise a larger proportion of cardiovascular events in women than in men.1 In terms of clinical impact, aspirin used for primary prevention is associated with a significance reduction in stroke women but not myocardial infarction in men.2 Differences in endogenous sex hormones have been hypothesized to underlie these substantial sex differences, but clinical data are limited on the relationship between endogenous levels and cardiovascular disease occurrence. Article, see p 97 In this issue, Glisic et al3 examine the relationship of endogenous sex hormone levels and carotid plaque composition, as well as incident stroke, in >2100 older men and women in the Rotterdam Study. Notably, presence of carotid atherosclerosis (carotid intimal–medial thickness of >2.0 mm on carotid screening) was more common among men than women in the study. Among those with established atherosclerosis, the prevalence of calcified plaques was similar in men and women, whereas women were less likely to have a lipid core (36.9% of women; 49.5% of men) and less likely to have intraplaque hemorrhage than men (29.0% of women; 40.0% of men). Endogenous hormones, specifically estradiol and testosterone, were correlated with carotid plaque composition. Higher estradiol levels were associated with increased odds of a lipid core in carotid plaque in both men and women. Women with detectable estradiol levels had a 58% increased odds of having intraplaque hemorrhage compared with women with low estradiol, whereas higher total testosterone levels were associated with decreased odds. No relationship was observed for total testosterone and carotid plaque composition features in men.3 Endogenous hormones were also related to incident stroke in women. Among women with carotid plaque, …
The IBM Speaker Recognition System: Recent Advances and Error Analysis

We present the recent advances along with an error analysis of the IBM speaker recognition system for conversational speech. Some of the key advancements that contribute to our system include: a nearest-neighbor discriminant analysis (NDA) approach (as opposed to LDA) for intersession variability compensation in the i-vector space, the application of speaker and channel-adapted features derived from an automatic speech recognition (ASR) system for speaker recognition, and the use of a DNN acoustic model with a very large number of output units (~10k senones) to compute the frame-level soft alignments required in the i-vector estimation process. We evaluate these techniques on the NIST 2010 SRE extended core conditions (C1-C9), as well as the 10sec-10sec condition. To our knowledge, results achieved by our system represent the best performances published to date on these conditions. For example, on the extended tel-tel condition (C5) the system achieves an EER of 0.59%. To garner further understanding of the remaining errors (on C5), we examine the recordings associated with the low scoring target trials, where various issues are identified for the problematic recordings/trials. Interestingly, it is observed that correcting the pathological recordings not only improves the scores for the target trials but also for the nontarget trials.
Influence of Maternal Age on the Fitness of Progeny in the Rice Weevil, Sitophilus oryzae (Coleoptera: Curculionidae)

Abstract We studied the effects of maternal age on fitness of progeny in the rice weevil, Sitophilus oryzae L. (Coleoptera: Curculionidae). Five-, 20-, and 50-d-old female rice weevils were used to study the effects of maternal age on the lifetime fecundity and longevity of their daughters. In addition, we determined the effects of maternal age on the weight and survivorship of daughters’ progeny. Daughters of 5- and 20-d-old weevils lived longer, and the numbers and weights of the progeny of these daughters were higher than for daughters of 50-d-old weevils. Survivorship of immature grand-offspring of 5-, 20-, and 50-d-old female weevils was similar. None of the fitness characteristics of the daughters and grand-offspring of 5- and 20-d-old weevils that were measured differed significantly. We believe maternal age effects on rice weevil progeny fitness may at least partly be acting through maternal age effect on egg size. Individuals that developed from younger 5- and 20-d-old weevils had a greater fitness than those produced by older 50-d-old females. Our study shows maternal age is impacting life history parameters that influence population dynamics across generations. Therefore, maternal age could significantly affect population development and have far reaching implications for pest management and simulation modeling of rice weevil populations.
Capacitance-based wireless sensor mote for snail pest detection

Pests due to terrestrial mollusks cause serious damage, both economic and ecological, in various types of agricultural plantations. In this paper we develop a low cost capacitive sensor that wirelessly communicates with the base, to monitor the activity of land snails. Once implemented physically, it has been tested in a controlled miniplot with favorable results.
Mycobacteria use their surface-exposed glycolipids to infect human macrophages through a receptor-dependent process Published, JLR Papers in Press, December 1, 2004. DOI 10.1194/jlr.M400308-JLR200

Two subfamilies of the polar glycopeptidolipids (GPLs) located on the surface of Mycobacterium smegmatis, along with unknown phospholipids, were recently shown to participate in the nonopsonic phagocytosis of mycobacteria by human macrophages (Villeneuve, C., G. Etienne, V. Abadie, H. Montrozier, C. Bordier, F. Laval, M. Daffe, I. Maridonneau-Parini, and C. Astarie-Dequeker. 2003. Surface-exposed glycopeptidolipids of Mycobacterium smegmatis specifically inhibit the phagocytosis of mycobacteria by human macrophages. Identification of a novel family of glycopeptidolipids. J. Biol. Chem. 278: 51291–51300). As demonstrated herein, a phospholipid mixture that derived from the methanol-insoluble fraction inhibited the phagocytosis of M. smegmatis. Inhibition was essentially attributable to phosphatidylinositol mannosides (PIMs), namely PIM2 and PIM6, because the purified phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol were inactive. This was further confirmed using purified PIM2 and PIM6 from M. bovis BCG that decreased by half the internalization of M. smegmatis. Both compounds also inhibited the uptake of M. tuberculosis and M. avium but had no effect on the internalization of zymosan used as a control particle of the phagocytic process. When coated on latex beads, PIM2 and polar GPL (GPL III) favored the particle entry through complement receptor 3. GPL III, but not PIM2, also directed particle entry through the mannose receptor. Therefore, surface-exposed mycobacterial PIM and polar GPL participate in the receptor-dependent internalization of mycobacteria in human macrophages.
Prevalence of Abnormal Anal Cytology and High-Grade Squamous Intraepithelial Lesions Among a Cohort of HIV-Infected Men Who Have Sex With Men

BACKGROUND: The incidence of anal cancer among HIV-infected patients is higher than that in other populations. Anal high-grade squamous intraepithelial lesions are considered precursors to invasive squamous-cell carcinomas and are strongly associated to high-risk human papillomavirus infection. OBJECTIVE: The aim of this study is to determine the prevalence of anal high-grade squamous intraepithelial lesions through screening based on cytology and high-resolution anoscopy with biopsy in a cohort of HIV-infected men who have sex with men. DESIGN: This investigation is an observational cross-sectional cohort study. SETTING: The study was conducted in the HIV unit of a tertiary hospital in Spain. PATIENTS: Three hundred HIV-infected men who have sex with men participated. Physical examination led to a diagnosis of perianal squamous-cell carcinoma and high-grade squamous intraepithelial lesions in 2 patients who were then excluded. INTERVENTIONS: Anal liquid cytology was performed. Patients with cytological abnormalities underwent high-resolution anoscopy and biopsy. MAIN OUTCOME MEASURE: The primary outcome measured was biopsy-proven high-grade squamous intraepithelial lesions. RESULTS: The median age was 41 ± 10.5 years. The mean and nadir CD4 cell counts were 651 ± 205 cells/mm3 (interquartile range, 438–800) and 273 ± 205 cells/mm3 (interquartile range, 131–362). High-risk human papillomavirus was detected in 80.9% of patients, and human papillomavirus 16 was detected in 35.9% of patients. The mean number of human papillomavirus genotypes was 4.6 ± 2.9 (CI, 2–6). Anal cytology was abnormal in 40.9% of patients (n = 122/298; interquartile range, 35.4%–46.6%). High-resolution anoscopy and biopsies were performed in 119 patients. The results of histological analyses were as follows: normal, 7.7% (n = 23); condyloma, 4.3% (n = 13); anal intraepithelial neoplasia 1, 5.7% (n = 17); anal intraepithelial neoplasia 2, 14% (n = 42); and anal intraepithelial neoplasia 3, 8% (n = 24). The overall prevalence of high-grade squamous intraepithelial lesions among patients with abnormal cytology was 54% (95% CI, 45.1%–62.8%). A diagnosis of high-grade squamous intraepithelial lesions was associated with human papillomavirus 16 and human papillomavirus 51 infection, and with detection of a higher number of human papillomavirus genotypes. LIMITATIONS: High-resolution anoscopy was only performed in patients with abnormal cytology. CONCLUSIONS: The prevalence of high-risk human papillomavirus infection and high-grade squamous intraepithelial lesions is high in our cohort. Physical examination enabled straightforward diagnosis of perianal high-grade squamous intraepithelial lesions and squamous-cell carcinoma in 2 patients.
Referential Translation Machines for Quality Estimation

We introduce referential translation machines (RTM) for quality estimation of translation outputs. RTMs are a computational model for identifying the translation acts between any two data sets with respect to a reference corpus selected in the same domain, which can be used for estimating the quality of translation outputs, judging the semantic similarity between text, and evaluating the quality of student answers. RTMs achieve top performance in automatic, accurate, and language independent prediction of sentence-level and word-level statistical machine translation (SMT) quality. RTMs remove the need to access any SMT system specific information or prior knowledge of the training data or models used when generating the translations. We develop novel techniques for solving all subtasks in the WMT13 quality estimation (QE) task (QET 2013) based on individual RTM models. Our results achieve improvements over last year’s QE task results (QET 2012), as well as our previous results, provide new features and techniques for QE, and rank 1st or 2nd in all of the subtasks.
Recurrence of brain tumours in patients treated with growth hormone: Analysis of KIGS (Pfizer International Growth Database)

Background: Growth hormone (GH) has been used successfully in the treatment of short stature secondary to GH deficiency in survivors of childhood brain tumours. There has been concern that GH might increase the risk of recurrence. Aim: To analyse KIGS (Pfizer International Growth Database) with respect to tumour recurrence in patients with brain tumours. Methods: Data for tumour recurrence were analysed retrospectively in 1038 patients with craniopharyngiomas, 655 with medulloblastomas, 113 with ependymomas, 297 with germinomas, and 400 with astrocytomas or gliomas. All patients had received recombinant human GH (Genotropin®, Pfizer Inc.). Results: Recurrence‐free survival rates were 63% at a follow‐up of 10.3 y in craniopharyngioma, 69% in 9.1 y in the glial tumours, 71% in 7.4 y in germinomas, 92% in 4.6 y in medulloblastomas and 89% in 2.5 y in ependymomas. Dose of GH and treatment modalities did not differ significantly between patients with and without recurrence.
The Relationship between Liquidity Risk and Credit Risk in Banks

This paper investigates the relationship between the two major sources of bank default risk: liquidity risk and credit risk. We use a sample of virtually all US commercial banks during the period 1998–2010 to analyze the relationship between these two risk sources on the bank institutional-level and how this relationship influences banks’ probabilities of default (PD). Our results show that both risk categories do not have an economically meaningful reciprocal contemporaneous or time-lagged relationship. However, they do influence banks’ probability of default. This effect is twofold: whereas both risks separately increase the PD, the influence of their interaction depends on the overall level of bank risk and can either aggravate or mitigate default risk. These results provide new insights into the understanding of bank risk and serve as an underpinning for recent regulatory efforts aimed at strengthening banks (joint) risk management of liquidity and credit risks.
Constant scalar curvature metrics on connected sums

The Yamabe problem (proved in 1984) guarantees the existence of a metric of constant scalar curvature in each conformal class of Riemannian metrics on a compact manifold of dimension n ≥ 3 , which minimizes the total scalar curvature on this conformal class. Let ( M ′ , g ′ ) and ( M ″ , g ″ ) be compact Riemannian n -manifolds. We form their connected sum M ′ # M ″ by removing small balls of radius ϵ from M ′ , M ″ and gluing together the 𝒮 n − 1 boundaries, and make a metric g on M ′ # M ″ by joining together g ′ , g ″ with a partition of unity. In this paper, we use analysis to study metrics with constant scalar curvature on M ′ # M ″ in the conformal class of g . By the Yamabe problem, we may rescale g ′ and g ″ to have constant scalar curvature 1 , 0 , or − 1 . Thus, there are 9 cases, which we handle separately. We show that the constant scalar curvature metrics either develop small necks separating M ′ and M ″ , or one of M ′ , M ″ is crushed small by the conformal factor. When both sides have positive scalar curvature, we find three metrics with scalar curvature 1 in the same conformal class.
Notes on the independence number in the Cartesian product of graphs

Every connected graph G with radius r(G) and independence number (G) obeys (G) r(G). Recently the graphs for which equality holds have been classied. Here we investigate the members of this class that are Cartesian products. We show that for non-trivial graphs G and H, (G2H) = r(G2H) if and only if one factor is a complete graph on two vertices, and the other is a nontrivial complete graph. We also prove a new (polynomial computable) lower bound (G2H) 2r(G)r(H) for the independence number and we classify graphs for which equality holds. The second part of the paper concerns independence irreducibility.
Clinical utility of ultrasound guidance for intra-articular knee injections: a review

Intra-articular corticosteroid and hyaluronic acid injections provide short-term symptom amelioration for arthritic conditions involving structural damage or degenerative changes in the knee. Conventional palpation-guided anatomical injections frequently result in inaccurate needle placement into extra-articular tissue and adjacent structures. The purpose of this review was to determine the effect of ultrasound guidance on the accuracy of needle placement, clinical outcomes, and cost-effectiveness in comparison with anatomical landmark-guided intra-articular large joint injections, with particular emphasis on the knee. A total of 13 relevant studies were identified; five studied the knee, seven studied the shoulder, one used both the knee and shoulder, and none studied the hip. Ultrasound was used in seven studies; the remaining studies utilized air arthrography, fluoroscopy, magnetic resonance arthrography, or magnetic resonance imaging. Across all studies (using all imaging modalities and all joints), needle placement accuracy ranged from 63% to 100% with ultrasound and from 39% to 100% with conventional anatomical guidance. Imaging guidance improved the accuracy of intra-articular injections of the knee (96.7% versus 81.0%, P < 0.001) and shoulder (97.3% versus 65.4%, P < 0.001). In particular, ultrasound guidance of knee injections resulted in better accuracy than anatomical guidance (95.8% versus 77.8%, P < 0.001), yielding an odds ratio of 6.4 (95% confidence interval 2.9–14). Ultrasound guidance notably improves injection accuracy in the target intra-articular joint space of large joints including the knee. The enhanced injection accuracy achieved with ultrasound needle guidance directly improves patient-reported clinical outcomes and cost-effectiveness.
Factors influencing the suitability of organ-cultured corneas for transplantation.

PURPOSE To assess the influence of donor and storage factors on the suitability of organ-cultured corneas for penetrating keratoplasty (PKP) using multifactorial regression analysis. METHODS Corneas (mean donor age, 57 years; standard deviation, 21 years) were stored by organ culture at 34 degrees C for up to 5 weeks (mean, 22 days; standard deviation, 6 days). The endothelium was assessed by light microscopy, and corneas with < 2200 cells/mm2 were considered unsuitable for PKP. RESULTS Of the 9250 corneas stored between 1992 and 1994, 59% were issued for PKP, 5% were discarded because of bacterial or fungal contamination, and 30% were unsuitable for PKP owing to endothelial deficiencies. Donor age had the strongest influence on suitability for PKP: > 80% of corneas from donors younger than 40 years of age were issued for PKP compared with only 45% of corneas from donors 80 years of age and older. There was an overall decline in the percentage of corneas suitable for PKP with increasing storage time, but the rate of this decline was inversely related to donor age. Cause of death and post mortem times to enucleation and to storage had only a small influence on suitability for PKP. CONCLUSIONS Criteria based on endothelial assessment rather than on donor age allow corneas from donors of all ages, stored by organ culture for extended periods, to be used for PKP. Organ culture also allows corneas with bacterial or fungal contamination to be identified and discarded before they are grafted.
Coexistence of multiple anomalies in the hepatobiliary system

The co-occurrence of several anomalies in the hepatobiliary system is uncommon. In the present study, hepatic lobe anomalies occurring in combination with hepatic artery and biliary variations were observed in an adult male cadaver. There are no previous reports in the literature on the coexistence of such anatomical variations. Preoperative diagnosis of such coexisting anomalies is very difficult. Hence, a thorough knowledge of these variations will enable surgeons to select the most appropriate hepatobiliary surgical procedure and postoperative management.
Mechanical properties of dual phase steel quenched in bitumenmedium

The mechanical properties of a dual phase steel treated in different intercritical windows and subjected to bitumen as the quenching medium was investigated. The viscosity of the quenchant was altered at several rate, the morphology of phases formed was characterized. Also, the quenched samples produced ferrite-martensite phases obtained at different intercritical windows. The tensile and hardness behaviour of the structures was examined; and the microstructures were characterized. It was observed that samples intercriticaly heat treated at 790°C and held for 60mins, bitumen quenched at 125°C, offers the highest impact toughness, while its counterpart at 730°C soaked for 30mins, bitumen quenched at 125°C offered the least impact toughness value. Sample intercriticaly treated at 790°C and held for 45mins in a 150°C quenching, offered the peak hardness factor. However, samples at 790°C held at 45mins and bitumen quenched at 150°C possessed relatively the best combination of tensile properties, hardness and impact energy. The water quenched samples at 790°C held for 60mins has the peak hardness value. The micrographs as well showed a uniformly distributed dual phase structure of ferrite and martensite at various volume fractions.
Some asymptotics of TQFT via skein theory

For each oriented surface $\Sigma$ of genus $g$ we study a limit of quantum representations of the mapping class group arising in TQFT derived from the Kauffman bracket. We determine that these representations converge in the Fell topology to the representation of the mapping class group on $\boH(\Sigma)$, the space of regular functions on the $SL(2,\C)$ representation variety with its hermitian structure coming from the symplectic structure of the SU(2)-representation variety. As a corollary, we give a new proof of the asymptotic faithfulness of quantum representations.
Development of normative human gait kinematics and kinetics database for Malaysian university students

Development of normaltive gait database catered for specific demographics are important to provide reference database to distinguish between normal and pathological gait parameters. In this project, an instrumented treadmill system was utilized to collect spatio-temporal parameters, and the Vertical Ground Reaction Forces (VGRFs) of Malaysian university students. Two (2) different movement were recorded, namely walking and running. In the initial findings of this study revealed that selected gait parameters were in agreement with published data available. It is anticipated that such database will be expended to cover more test subjects of different ethnicities to serve as reference database for human gait analysis in Malaysian context specifically, and the Asian context in general.