Miracle-dz/UniFAR-FTUs huggingface dataset:
THE +1245G/T POLYMORPHISMS IN THE COLLAGEN TYPE I ALPHA 1 (COL1A1) GENE IN POLISH SKIERS WITH ANTERIOR CRUCIATE LIGAMENT INJURY

Objectives The aim of this study was to examine the association of +1245G/T polymorphisms in the COL1A1 gene with ACL ruptures in Polish male recreational skiers in a case-control study. Methods A total of 138 male recreational skiers with surgically diagnosed primary ACL ruptures, all of whom qualified for ligament reconstruction, were recruited for this study. The control group comprised 183 apparently healthy male skiers with a comparable level of exposure to ACL injury, none of whom had any self-reported history of ligament or tendon injury. DNA samples extracted from the oral epithelial cells were genotyped for the +1245G/T polymorphisms using real-time PCR method. Results Genotype distributions among cases and controls conformed to Hardy-Weinberg equilibrium (p = 0.2469 and p = 0.33, respectively). There was a significant difference in the genotype distribution between skiers and controls (p = 0.045, Fisher's exact test). There was no statistical difference in allele distribution: OR 1.43 (0.91-2.25), p = 0.101 (two-sided Fisher's exact test). Conclusions The risk of ACL ruptures was around 1.43 times lower in carriers of a minor allele G as compared to carriers of the allele T.
Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding

Abstract Protein–DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (shape readout). The underlying mechanism of DNA shape readout involves the correlation between minor-groove width and electrostatic potential (EP). To probe this biophysical effect directly, rather than using minor-groove width as an indirect measure for shape readout, we developed a methodology, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in protein–DNA binding using massive sequencing data. The DNAphi method uses a sliding-window approach to mine results from non-linear Poisson–Boltzmann (NLPB) calculations on DNA structures derived from all-atom Monte Carlo simulations. We validated this approach, which only requires nucleotide sequence as input, based on direct comparison with NLPB calculations for available crystal structures. Using statistical machine-learning approaches, we showed that adding EP as a biophysical feature can improve the predictive power of quantitative binding specificity models across 27 transcription factor families. High-throughput prediction of EP offers a novel way to integrate biophysical and genomic studies of protein–DNA binding.
Evaluation of Bt-cotton Genotypes for Resistance to Cotton Leaf Curl Disease under High Inoculum Pressure in the Field and Using Graft Inoculation in Glasshouse

Bt-cotton germplasm, consisting of 75 genotypes was evaluated against cotton leaf curl disease (CLCuD) under high inoculum pressure in the field and using graft inoculation in glasshouse by visual symptom scoring assessments. None of the tested genotype was found disease free under both evaluation tests. Under field conditions in 2011, 3 genotypes were found resistant, 4 moderately resistant, 3 tolerant, 2 moderately susceptible and one susceptible; in 2012, 3 genotypes were tolerant, 7 moderately susceptible, 5 susceptible and 38 highly susceptible; in 2013, one was moderately susceptible and 51 were highly susceptible with varying degree of percent disease index (PDI) and severity index (SI). However, through graft evaluation in glasshouse, none of the graft inoculated plant was symptomless. All tested genotypes showed disease symptoms with SI values ranging between 5.0 and 6.0, and latent period between 12 and 14 days. Of the 75 genotypes evaluated using graft inoculation, 11 were found susceptible with SI values of 5.0 to 5.4 while remaining 64 were highly susceptible with SI values of 5.5 to 6.0. Inoculated plants of all tested genotypes exhibited severe disease symptoms within 10 days after the appearance of initial symptoms. No reduction in SI value was observed until the end of the experiment i.e., 90 days after grafting. Information generated under the present study clearly demonstrates that no sources of resistance to CLCuD are available among the tested Bt-cotton genotypes. So, a breeding programme is needed to introgress the CLCuD-resistance from other resistant sources to agronomically suitable Bt-cotton genotypes.
Cutting on triangle mesh: local model-based haptic display for dental preparation surgery simulation

A new method to realize stable and realistic cutting simulation using an impedance display haptic device and microcomputer is presented in this paper. Material removal or cutting simulation is a critical task in dental preparation surgery simulation. In this paper, a piecewise contact force model is proposed to approximately describe the cutting process. Challenging issues of minimizing the difference between the cutting simulation and haptic contact simulation are analyzed. The proposed contact-based simulation method is developed for a one-dimensional cutting task and can be expanded to three-dimensional cases. Local model-based multirate simulation cutting architecture is proposed and force control of the haptic device is decoupled from the cutting simulation loop, which can both ensure high fidelity of dynamical simulation as well as maintain stability of the haptic device. The cutting operation is realized using spherical and cylindrical shaped tools. An experiment based on the Phantom desktop proves that fidelity in one-dimensional cutting can be realized and stability in three-dimensional cutting can be ensured using the force-filtering method.
EVENODD: An Efficient Scheme for Tolerating Double Disk Failures in RAID Architectures

We present a novel method, that we call EVENODD, for tolerating up to two disk failures in RAID architectures. EVENODD employs the addition of only two redundant disks and consists of simple exclusive-OR computations. This redundant storage is optimal, in the sense that two failed disks cannot be retrieved with less than two redundant disks. A major advantage of EVENODD is that it only requires parity hardware, which is typically present in standard RAID-5 controllers. Hence, EVENODD can be implemented on standard RAID-5 controllers without any hardware changes. The most commonly used scheme that employes optimal redundant storage (i.e., two extra disks) is based on Reed-Solomon (RS) error-correcting codes. This scheme requires computation over finite fields and results in a more complex implementation. For example, we show that the complexity of implementing EVENODD in a disk array with 15 disks is about 50% of the one required when using the RS scheme. The new scheme is not limited to RAID architectures: it can be used in any system requiring large symbols and relatively short codes, for instance, in multitrack magnetic recording. To this end, we also present a decoding algorithm for one column (track) in error. >
Initial case report of an extracted tooth root used for lateral alveolar ridge augmentation.

OBJECTIVES Recent animal studies have indicated, that tooth roots reveal a structural and biological potential to serve as alternative autografts for localized ridge augmentation. This proof-of-concept initial report aimed at investigating, whether this new surgical concept may be applied to humans. MATERIAL & METHODS In one patient, who was in need for horizontal ridge augmentation, the roots of a retained upper wisdom tooth were separated and rigidly fixed at the defect site. After 24 weeks of submerged healing, the primary endpoint was defined as gain in ridge width (mm) being sufficient to place an adequately dimensioned titanium implant at the respective site. Secondary outcomes included safety assessments. RESULTS Soft tissue healing was uneventful during the entire observation period. Clinical re-entry at 24 weeks revealed, that the transplanted root was homogeneously incorporated at the former defect site and mainly replaced by a newly formed hard tissue. The gain in ridge width amounted to 4.5 mm and allowed for a successful implant placement with good primary stability. The procedure was not associated with any wound infection or adverse events. CONCLUSIONS This novel approach may be further investigated in implant site development procedures.
Opposite nucleotide usage biases in different parts of the Corynebacterium diphtheriae spaC gene

In this work we described a bacterial open reading frame with two different directions of nucleotide usage biases in its two parts. The level of GC-content in third codon positions (3GC) is equal to 40.17 ± 0.22% during the most of the length of Corynebacterium diphtheriae spaC gene. However, in the 3'-end of the same gene (from codon #1600 to codon #1873) 3GC level is equal to 64.61 ± 0.91%. Using original methodology ('VVTAK Sliding window' and 'VVTAK VarInvar') we approved that there is an ongoing mutational AT-pressure during the most of the length of spaC gene (up to codon #1599), and there is an ongoing mutational G-pressure in the 3′-end of spaC. Intragenic promoters predicted by three different methods may be the cause of the differences in preferable types of nucleotide mutations in spaC parts because of their autonomous transcription.
Professionalism perspectives among medical students of a novel medical graduate school in Malaysia

Defining professionalism in this constantly evolving world is not easy. How do you measure degrees of benevolence and compassion? If it is so obvious to our profession, what professionalism is, then why is it so difficult to teach it to medical students and residents? Today’s definition of medical professionalism is evolving – from autonomy to accountability, from expert opinion to evidence-based medicine, and from self-interest to teamwork and shared responsibility. However, medical professionalism is defined as the basis for the trust in the patient–physician relationship, caring and compassion, insight, openness, respect for patient dignity, confidentiality, autonomy, presence, altruism, and those qualities that lead to trust-competence, integrity, honesty, morality, and ethical conduct. The purpose of this study is to explore professionalism in terms of its fundamental elements among medical students of Universiti Sultan Zainal Abidin (UniSZA). This was a cross-sectional study carried out on medical students of UniSZA. The study population included preclinical and clinical medical students of UniSZA from Year I to Year V of academic session 2014/2015. The simple random sampling technique was used to select the sample. Data were collected using a validated instrument. The data were then compiled and analyzed using SPSS Version 21. Out of 165 questionnaires distributed randomly among Year I to Year V medical students of UniSZA, 144 returned, giving a response rate of 87%. Among the study participants, 38% (54) and 62% (90) were males and females, respectively. The grand total score was 170.92±19.08. A total of 166.98±20.15 and 173.49±18.09 were the total professionalism score of male and female study participants, respectively, with no statistically significant (P=0.61) differences. This study found almost similar levels of familiarity with all fundamental issues of professionalism with no statistically (P>0.05) significant differences. Medical faculty members should give more effort for the professional development of medical doctor. Henceforth, researchers believe and expect that the country will produce more rational and holistic medical doctors.
Antioxidant vitamin and mineral supplements for age-related macular degeneration.

BACKGROUND It has been proposed that antioxidants may prevent cellular damage in the retina by reacting with free radicals produced in the process of light absorption. OBJECTIVES The objective of this review is to assess the effects of antioxidant vitamin and/or mineral supplementation on the progression of age-related macular degeneration. SEARCH STRATEGY The Cochrane Controlled Trials Register - CENTRAL/CCTR, which contains the Cochrane Eyes and Vision Group specialised register (Cochrane Library Issue 3 2001), MEDLINE (1966 to August 2001), EMBASE (1980 to September 2001), the Science Citation Index, and the reference lists of relevant articles were searched. Investigators of included studies were contacted for further information. SELECTION CRITERIA Randomised trials comparing an antioxidant vitamin and/or mineral supplement (alone or in combination) to control in people with age-related macular degeneration are included in this review. DATA COLLECTION AND ANALYSIS The reviewer extracted data and assessed trial quality. Due to the variable methods of collecting and presenting outcome data, no statistical summary measure was calculated. MAIN RESULTS Seven trials, which randomised 4119 people with signs of age-related macular degeneration, are included in this review. One unpublished trial of zinc supplementation (170 participants) is awaiting assessment. The majority of people (88%) were randomised in one trial that was conducted in a relatively well-nourished American population. This trial found a modest beneficial effect of antioxidant and zinc supplementation on progression to advanced age-related macular degeneration (odds ratio 0.72, 99% confidence interval 0.52 to 0.98). People supplemented with antioxidants and zinc were less likely to lose 15 or more letters of visual acuity (equivalent to a doubling of the visual angle) (odds ratio 0.79, 99% confidence interval 0.60 to 1.04). The other six trials in this review were small and the results were inconsistent. REVIEWER'S CONCLUSIONS The evidence as to the effectiveness of antioxidant vitamin and mineral supplementation in halting the progression of age-related macular degeneration is dominated by one large trial in a relatively well-nourished American population that showed modest benefit in people with moderate to severe signs of the disease. There is no evidence at present that people with early signs of the disease should take supplementation, however, current studies are underpowered to answer that question. The generalisability of these findings to other populations with different nutritional status is not known. Further large well-conducted randomised controlled trials in other populations are required.
Biotyping and Genotyping (MLVA16) of Brucella abortus Isolated from Cattle in Brazil, 1977 to 2008

Brucellosis is a worldwide distributed zoonosis that causes important economic losses to animal production. In Brazil, information on the distribution of biovars and genotypes of Brucella spp. is scarce or unavailable. This study aimed (i) to biotype and genotype 137 Brazilian cattle isolates (from 1977 to 2008) of B. abortus and (ii) to analyze their distribution. B. abortus biovars 1, 2 and 3 (subgroup 3b) were confirmed and biovars 4 and 6 were first described in Brazil. Genotyping by the panel 1 revealed two groups, one clustering around genotype 40 and another around genotype 28. Panels 2A and 2B disclosed a high diversity among Brazilian B. abortus strains. Eighty-nine genotypes were found by MLVA16. MLVA16 panel 1 and 2 showed geographic clustering of some genotypes. Biotyping and MLVA16 genotyping of Brazilian B. abortus isolates were useful to better understand the epidemiology of bovine brucellosis in the region.
Physical activity using wrist‐worn accelerometers: comparison of dominant and non‐dominant wrist

The purpose of this study was to determine whether there is a difference in physical activity assessment between a wrist‐worn accelerometer at the dominant or non‐dominant arm. The secondary purpose was to assess the concurrent validity of measures of physical activity from the wrist‐worn accelerometer and the waist‐worn accelerometer. Forty adults wore three accelerometers simultaneously, one on the waist and one each on the non‐dominant wrist and dominant wrist, respectively, for 24 consecutive hours of free‐living conditions. Data were uploaded from the monitor to a computer following a 1‐day test period. There were no significant differences in physical activity when comparing the dominant versus the non‐dominant wrist, regardless of axis (P>0·05). Mean daily accelerometer output data from both wrists were strongly correlated with average counts per minute from the ActiGraph worn around the waist (r = 0·88, P<0·001). Findings suggest that the choice to wear the accelerometer on the non‐dominant or dominant wrist has no impact on results. Data from this study contribute to the knowledge of how to best assess physical activity habits.
The complexity of online memory checking

We consider the problem of storing a large file on a remote and unreliable server. To verify that the file has not been corrupted, a user could store a small private (randomized) "fingerprint" on his own computer. This is the setting for the well-studied authentication problem in cryptography, and the required fingerprint size is well understood. We study the problem of sub-linear authentication: suppose the user would like to encode and store the file in a way that allows him to verify that it has not been corrupted, but without reading the entire file. If the user only wants to read t bits of the file, how large does the size s of the private fingerprint need to be? We define this problem formally, and show a tight lower bound on the relationship between s and t when the adversary is not computationally bounded, namely: s /spl times/ t = /spl Omega/(n), where n is the file size. This is an easier case of the online memory checking problem, introduced by Blum et al. in 1991, and hence the same (tight) lower bound applies also to that problem. It was previously shown that when the adversary is computationally bounded, under the assumption that one-way functions exist, it is possible to construct much better online memory checkers and sub-linear authentication schemes. We show that the existence of one-way functions is also a necessary condition: even slightly breaking the s /spl times/ t = /spl Omega/(n) lower bound in a computational setting implies the existence of one-way functions.
Orange-fleshed sweet potato : the history, adoption, effect and potential of a nutritionally superior staple crop in Mozambique

The purpose of this research is to understand the history and effectiveness of orangefleshed sweet potato (OFSP) interventions in Mozambique as well as to identify factors that influence the adoption and retention of this crop. To achieve this purpose, an indepth literature review was conducted to collate a time line of events surrounding OFSP introduction. Primary research was carried out to explore remaining challenges associated with improving adoption and retention levels and involved interviews and focus groups with 95 participants including farmers, consumers, and market vendors of OFSP. Field research was carried out in three provinces of Mozambique over a nine month period in 2015 with funding provided by the Fulbright US student program. Interviews and focus groups were translated and transcribed verbatim by the researcher and were analyzed by a team of authors to understand the site-specific factors affecting farmer willingness and ability to procure, preserve, cultivate, and distribute OFSP varieties, with a particular interest in the retention of planting material over time. Diffusion of Innovations Theory was utilized in the research design, analysis, and reporting. Results indicate that a wide variety of factors influence adoption and retention of orange-fleshed sweet potato, including: awareness of health benefits; organoleptic qualities and taste preferences; access to planting material; perceived difference in agronomic traits, including pest and drought resistance, time to root maturity, and vine development; dependence on nongovernment organizations or neighbors for planting material; lack of access to capital for inputs and labor; unstable markets and fluctuating prices; and varying levels of sharing of information and planting material across farmer networks. Future research should focus on mechanisms to increase year-round availability of planting material, improved drought and pest tolerance for OFSP, understanding farmer preference for vine and leaf development, renewed emphasis on nutritional benefits and cooking methods for sweet potato derivatives, gender dynamics of sweet potato commercialization, and farmer training on improved agricultural techniques that highlights the agronomic similarities between OFSP and WFSP to avoid perceptions that OFSP production is more labor intensive.
Expression and enforcement of confidentiality policy in active databases

Many research works focused on modeling relational database management systems (DBMS) that support multilevel security (MLS) policies. However, most of these previous proposals only consider static aspects of relational databases and do not address dynamicity provided by mechanisms like triggers. Since such mechanisms introduced specific security problems, in particular they create new information flows, it is necessary to extend traditional MLS models designed for relational databases to handle these problems. However, it has been shown in many papers that triggers lack a formal model to support them and so they are not free of ambiguities. To address these theoretical limitations of trigger, our work is based on a formal model that applies MLS policies to active databases. Active databases provide a more expressive and formal framework than triggers. In this paper, we first define an information flow model for active databases. Based on this security model, we then present security requirements that are sufficient to prevent illegal information flows and prove them using the B method.
The Positioning and Dynamics of Origins of Replication in the Budding Yeast Nucleus

We have analyzed the subnuclear position of early- and late-firing origins of DNA replication in intact yeast cells using fluorescence in situ hybridization and green fluorescent protein (GFP)–tagged chromosomal domains. In both cases, origin position was determined with respect to the nuclear envelope, as identified by nuclear pore staining or a NUP49-GFP fusion protein. We find that in G1 phase nontelomeric late-firing origins are enriched in a zone immediately adjacent to the nuclear envelope, although this localization does not necessarily persist in S phase. In contrast, early firing origins are randomly localized within the nucleus throughout the cell cycle. If a late-firing telomere-proximal origin is excised from its chromosomal context in G1 phase, it remains late-firing but moves rapidly away from the telomere with which it was associated, suggesting that the positioning of yeast chromosomal domains is highly dynamic. This is confirmed by time-lapse microscopy of GFP-tagged origins in vivo. We propose that sequences flanking late-firing origins help target them to the periphery of the G1-phase nucleus, where a modified chromatin structure can be established. The modified chromatin structure, which would in turn retard origin firing, is both autonomous and mobile within the nucleus.