Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational Analysis of Different Regions in the Coxsackievirus 2B Protein

The coxsackievirus 2B protein is a small hydrophobic protein (99 amino acids) that increases host cell membrane permeability, possibly by forming homo-multimers that build membrane-integral pores. Previously, we defined the functional role of the two hydrophobic regions HR1 and HR2. Here, we investigated the importance of regions outside HR1 and HR2 for multimerization, increasing membrane permeability, subcellular localization, and virus replication through analysis of linker insertion and substitution mutants. From these studies, the following conclusions could be drawn. (i) The hydrophilic region (58RNHDD62) between HR1 and HR2 is critical for multimerization and increasing membrane permeability. Substitution analysis of Asn61 and Asn62 demonstrated the preference for short polar side chains (Asp, Asn), residues that are often present in turns, over long polar side chains (Glu, Gln). This finding supports the idea that the hydrophilic region is involved in pore formation by facilitating a turn between HR1 and HR2 to reverse chain direction. (ii) Studies undertaken to define the downstream boundary of HR2 demonstrated that the aromatic residues Trp80 and Trp82, but not the positively charged residues Arg81, Lys84, and Lys86 are important for increasing membrane permeability. (iii) The N terminus is not required for multimerization but does contribute to the membraneactive character of 2B. (iv) The subcellular localization of 2B does not rely on regions outside HR1 and HR2 and does not require multimerization. (v) Virus replication requires both the membrane-active character and an additional function of 2B that is not connected to this activity.
Investigating the relationship between prenatal growth and postnatal outcomes: a systematic review of the literature

Theories regarding the relationship between pre- and postnatal growth and programming of health have been based on characteristics at birth, with little or no reference to the patterns of growth occurring in utero. Review of the literature to identify studies using ultrasonographically obtained fetal dimensions to track prenatal growth and relate these patterns of growth to postnatal anthropometry and cardiovascular and metabolic risk factors. Review of Medline, Scopus and Proquest for studies reporting on ultrasonographically derived estimates of fetal growth and their association with postnatal anthropometry, body composition or cardiovascular and metabolic risk factors. Quality of papers were assessed using the method developed by Downs and Black. Twenty-nine studies met the inclusion criteria, with a mean score of high quality. Twenty of the studies had follow-up in infancy, five in childhood, three in adolescence and one in adulthood. The associations observed suggest that centile tracking may occur early in pregnancy though whether this is as early as the first trimester is uncertain. The second trimester may be a critical period for the programming of blood pressure and abdominal circumference may be the most sensitive fetal dimension to indicate any programming.
Power and type I error results for a bias‐correction approach recently shown to provide accurate odds ratios of genetic variants for the secondary phenotypes associated with primary diseases

We recently proposed a bias correction approach to evaluate accurate estimation of the odds ratio (OR) of genetic variants associated with a secondary phenotype, in which the secondary phenotype is associated with the primary disease, based on the original case‐control data collected for the purpose of studying the primary disease. As reported in this communication, we further investigated the type I error probabilities and powers of the proposed approach, and compared the results to those obtained from logistic regression analysis (with or without adjustment for the primary disease status). We performed a simulation study based on a frequency‐matching case‐control study with respect to the secondary phenotype of interest. We examined the empirical distribution of the natural logarithm of the corrected OR obtained from the bias correction approach and found it to be normally distributed under the null hypothesis. On the basis of the simulation study results, we found that the logistic regression approaches that adjust or do not adjust for the primary disease status had low power for detecting secondary phenotype associated variants and highly inflated type I error probabilities, whereas our approach was more powerful for identifying the SNP‐secondary phenotype associations and had better‐controlled type I error probabilities. Genet. Epidemiol. 2011. © 2011 Wiley Periodicals, Inc. 35:739‐743, 2011
Repetitive TMS of the temporo-parietal junction disrupts participant’s expectations in a spontaneous Theory of Mind task

Abstract A recent debate about Theory of Mind (ToM) concerns whether spontaneous and explicit mentalizing are based on the same mechanisms. However, only a few neuroimaging studies have investigated the neural bases of spontaneous ToM, with inconsistent results. The present study had two goals: first, to investigate whether the right Temporo-Parietal Junction (rTPJ) is crucially involved in spontaneous ToM and second, to gain insight into the role of the rTPJ in ToM. For the first time, we applied rTMS to the rTPJ while participants were engaged in a spontaneous false belief task. Participants watched videos of a scene including an agent who acquires a true or false belief about the location of an object. At the end of the movie, participants reacted to the presence of the object. Results show that, during stimulation of the control site, RTs were affected by both the participant’s expectations and the belief of the agent. Stimulation of the rTPJ significantly modulated task performance, supporting the idea that spontaneous ToM, as well as explicit ToM, relies on TPJ activity. However, we did not observe a disruption of the representation of the agent’s belief. Rather, the stimulation interfered with participant’s predictions, supporting the idea that rTPJ is crucially involved in self-other distinction.
Soft and Hard Tissue Changes Around Laser Microtexture Single Tooth Implants—A Clinical and Radiographic Evaluation

Purpose: To investigate the periodontal parameters that affect the soft and hard tissues around Laser microtextured single tooth implants at 18 months after loading. Methods: Twenty Laser Lok implants were placed in 20 single missing tooth sites using a 2-stage protocol. Clinical Parameters included Plaque Index (PI), Gingival Index (GI), Probing Pocket Depth (PPD), Bleeding on Probing (BOP), and Crestal Bone Loss (CBL). Clinical and radiographic evaluation was done at loading, 12 months and 18 months after loading. The data collected were analyzed statistically. Results: The PI and GI during the entire follow-up period were well controlled. Eighty-six percent of implant sites were free of BOP at loading and 87% of sites were free of BOP at 18 months. A significant increase in PPD was not observed. The mean CBL was 0.59 mm at the time of loading, 0.80 mm at 12 months, and 1.06 mm at 18 months. Conclusion: The Laser Lok implants showed minimal CBL at 18 months than the commonly accepted 1.5 to 2.0 mm. The periimplant soft tissue stability was maintained throughout the study.
Effect of prophylactic intraocular pressure-lowering medication on intraocular pressure spikes after intravitreal injections.

OBJECTIVE To determine if prophylactic use of intraocular pressure (IOP)-lowering medication is effective in reducing the IOP spikes after intravitreal injections of pegaptanib, bevacizumab, and ranibizumab. METHODS Seventy-one patients with exudative age-related macular degeneration received intravitreal injections of 1 of 3 anti-vascular endothelial growth factor medications: 30 patients received pegaptanib (0.09 mL), 47 patients received bevacizumab (0.05 mL), and 42 patients received ranibizumab (0.05 mL). Intraocular pressure-lowering medication, 1 hour prior to the injection, was used 63%, 74%, and 66% of the time in eyes that received pegaptanib, ranibizumab, and bevacizumab, respectively. Intraocular pressure was measured prior to injection, within 1 minute after injection, and every 5 to 10 minutes until the pressure was reduced to a safe level. RESULTS All 3 intravitreal injections caused significant initial IOP spikes (mean [SD] IOP of 38.5 [11.56] mm Hg in the pegaptanib group, 37.75 [8.36] mm Hg in the ranibizumab group, and 34.88 [10.45] mm Hg in the bevacizumab group). The IOP reduced to less than 30 mm Hg in all 3 groups within 20 minutes. Prophylactic medication did not prevent postinjection IOP spikes. Patients with and without glaucoma showed a similar rate of IOP normalization over time in all 3 groups. CONCLUSION Intraocular pressure spikes after intravitreal injection of pegaptanib, ranibizumab, and bevacizumab are common and in most cases transient. Routine prophylactic use of IOP-lowering medications is essentially ineffective in preventing IOP spikes after intravitreal injection of pegaptanib, ranibizumab, and bevacizumab and therefore not necessary before the injection.
Visual Protection of HEVC Video by Selective Encryption of CABAC Binstrings

This paper presents one of the first methods allowing the protection of the newly emerging video codec HEVC (High Efficiency Video Coding). Visual protection is achieved through selective encryption (SE) of HEVC-CABAC binstrings in a format compliant manner. The SE approach developed for HEVC is different from that of H.264/AVC in several aspects. Truncated rice code is introduced for binarization of quantized transform coefficients (QTCs) instead of truncated unary code. The encryption space (ES) of binstrings of truncated rice codes is not always dyadic and cannot be represented by an integer number of bits. Hence they cannot be concatenated together to create plaintext for the CFB (Cipher Feedback) mode of AES, which is a self-synchronizing stream cipher for so-called AES-CFB. Another challenge for SE in HEVC concerns the introduction of context, which is adaptive to QTC. This work presents a thorough investigation of HEVC-CABAC from an encryption standpoint. An algorithm is devised for conversion of non-dyadic ES to dyadic, which can be concatenated to form plaintext for AES-CFB. For selectively encrypted binstrings, the context of truncated rice code for binarization of future syntax elements is guaranteed to remain unchanged. Hence the encrypted bitstream is format-compliant and has exactly the same bit-rate. The proposed technique requires very little processing power and is ideal for playback on hand held devices. The proposed scheme is acceptable for DRM of a wide range of applications, since it protects the contour and motion information, along with texture. Several benchmark video sequences of different resolutions and diverse contents were used for experimental evaluation of the proposed algorithm. A detailed security analysis of the proposed scheme verified the validity of the proposed encryption scheme for content protection in a wide range of applications.
BMI upon discharge from hospital and its relationship with survival: an observational study utilising linked patient records

Objective Current advice for patients being discharged from hospital suggests a body mass index of 18.5 to 24 kgm−2, although this aspirational target may often not be achieved. We examined the relationship between body mass index on discharge from hospital and subsequent mortality over a maximum follow-up of 3.8 years. Design We conducted a survival analysis using linked hospital records data with national hospital episode statistics and national death certification data. Participants & Setting The analysis included adult patients who were admitted to University Hospitals Birmingham NHS Foundation Trust for a period of over 24 h during 2011, excluding day cases and regular day case attenders. Main outcome measures The relationship between body mass index and mortality at medium term was estimated separately in both men and women, after accounting for case-mix. Results For both males and females, the relationship between body mass index at discharge and the loge hazard of death was strongly non-linear (p = 0.0002 for females and p < 0.0001 for males) and predictive (both p < 0.0001). In all models, the optimal body mass index range associated with best survival was 25 to 35 kgm−2, with a sharp increase in risk for lower body mass index. Conclusions There was little evidence to support current aspirational body mass index targets in the discharge population. Hospitals should ensure adequate nutrition especially among those with a reduced body mass index.
The effect of smoking on periodontal bone regeneration: a systematic review and meta-analysis.

BACKGROUND The effect of smoking on soft tissues after periodontal treatment has been extensively studied. However, little focus has been placed on the impact of smoking on bone regeneration after treatment. The aim of this review is to systematically assess the effect of smoking on bone regeneration after periodontal treatment. METHODS A protocol was established and studies were sourced from five electronic databases. Screening, data abstraction, and quality assessment was conducted by two review authors. Prospective and retrospective clinical studies assessing bone regeneration in smokers and non-smokers after periodontal therapy were selected. In addition, arms of clinical trials comparing different interventions that reported results separately for smokers and non-smokers were also included. Primary outcome measures were based on clinical and/or radiographic indicators of bone regeneration after periodontal therapy. The review and meta-analysis followed many of the recommendations outlined in the preferred reporting items for systematic reviews and meta-analyses statement. RESULTS Six of 10 studies included in this review concluded that smoking negatively influenced bone regeneration. A meta-analysis of a subgroup of three studies demonstrated that smoking resulted in significantly less bone gain (P = 0.03) as measured by a change in the probing bone level after the treatment of intrabony defects with guided tissue regeneration. The meta-analysis showed a standardized mean difference of -2.05 (95% confidence interval: -2.64 to -1.47) using the random-effects model. CONCLUSIONS Smoking has a negative effect on bone regeneration after periodontal treatment. Patients should be advised that their smoking habit may result in poorer bone regeneration after periodontal treatment.
Falls, poisonings, burns, and road traffic injuries in urban Peruvian children and adolescents: a community based study

Objectives: To identify individual and household characteristics associated with serious falls, poisonings, burns and road traffic injuries (RTIs) for children in Lima, Peru. Methods: 5061 households consisting of 10 210 children were included in this community based, cross-sectional study in San Juan de Miraflores (SJM), a low income, urban district of Lima, Peru. Households were eligible if there was a consenting adult and at least one resident child aged ⩽18 years. A door to door survey was conducted in SJM, collecting childhood injury, demographic, and socioeconomic data. Analysis was done at the individual and household level for injuries severe enough to have required medical consultation. Results: The greatest burden of injury was from falls and RTIs. For individuals, male gender and age were the most important predictors of injuries. Households in which multiple injuries were reported were more likely to be poor (odds ratio (OR) 1.66, 95% CI 1.24 to 2.22) and overcrowded (OR 1.88, 95% CI 1.20 to 2.94). The occurrence of serious falls, poisonings, burns, and pedestrian RTIs significantly increased the likelihood of a second serious injury in the home (adjusted ORs ranged between 1.88 and 2.99). Conclusion: All children from households in which an unintentional injury has occurred appear to have an increased likelihood of future injury; such high risk households may be readily identifiable in the clinical setting. Interventions in this environment designed to prevent subsequent injuries merit further investigation.
Pseudotumor cerebri from sinus venous thrombosis, associated with polycystic ovary syndrome and hereditary hypercoagulability

Objective. The association of pseudotumor cerebri, visual impairment, hypothyroidism, polycystic ovary syndrome (PCOS), and a hypercoagulable state due to a factor V and a prothrombin mutation has not been reported previously. Case report. A 20-year-old obese woman developed menstrual cycle irregularities since age 14 years, initially bitemporal and latter diffuse headache since age 14 years, and bilateral visual impairment, described as sparkling black points. Ophthalmologically there was a recurrent papilledema. Clinical neurologic investigations revealed sore neck muscles and hirsutism. Magnetic resonance imaging of the brain, orbita and cervical spine, and investigations of cerebrospinal fluid were non-informative. Visually evoked potentials revealed demyelination of the optic nerves. Gynecologic investigations revealed PCOS and endocrinologic investigations hypothyroidism and hyperandrogenism. Tests for thrombophilia disclosed a heterozygote state for the G1.697A factor V Leiden and the G20.210A prothrombin mutation. A possible relationship between pseudotumor cerebri and the ophthalmologic, gynecologic, endocrinologic and coagulation abnormalities is discussed. Conclusions. For the first time we describe the association of pseudotumor cerebri, optic nerve demyelination, PCOS, other endocrinologic abnormalities, and thrombophilia due to a factor V and prothrombin mutation. A causal relationship between these abnormalities remains elusive.
Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics

Many of the antibiotics used today are made by a group of bacteria called Streptomyces. Streptomycetes evolved about 450 million years ago as branched filamentous organisms adapted to the utilization of plant remains. They reproduce by sending up specialized aerial branches, which form spores. Aerial growth is parasitic on the primary colony, which is digested and reused for aerial growth. The reproductive phase is coordinated with the secretion of antibiotics, which may protect the colony against invading bacteria during aerial growth. A clue to the integration of antibiotic production and aerial growth is provided by bldA mutants, which are defective in both processes. These mutants lack the ability to translate a particularly rare codon, UUA, in the genetic code. The UUA codon (TTA in DNA) is present in several regulatory genes that control sets of antibiotic production genes, and in one, bldH that controls aerial mycelium formation. The regulatory genes for antibiotic production are all involved in self-reinforcing regulatory systems that potentially amplify the regulatory significance of small changes in the efficiency of translation of UUA codons. One of the regulatory targets of bldH is an extracellular protease inhibitor protein that is likely to delay the digestion of the primary biomass until the colony is ready for aerial growth. The use of the UUA codon to orchestrate different aspects of extracellular biology appeared very early in Streptomyces evolution.
Effect of a provincial system of stroke care delivery on stroke care and outcomes

Background: Systems of stroke care delivery have been promoted as a means of improving the quality of stroke care, but little is known about their effectiveness. We assessed the effect of the Ontario Stroke System, a province-wide strategy of regionalized stroke care delivery, on stroke care and outcomes in Ontario, Canada. Methods: We used population-based provincial administrative databases to identify all emergency department visits and hospital admissions for acute stroke and transient ischemic attack from Jan. 1, 2001, to Dec. 31, 2010. Using piecewise regression analyses, we assessed the effect of the full implementation of the Ontario Stroke System in 2005 on the proportion of patients who received care at stroke centres, and on rates of discharge to long-term care facilities and 30-day mortality after stroke. Results: We included 243 287 visits by patients with acute stroke or transient ischemic attack. The full implementation of the Ontario Stroke System in 2005 was associated with an increase in rates of care at stroke centres (before implementation: 40.0%; after implementation: 46.5%), decreased rates of discharge to long-term care facilities (before implementation: 16.9%; after implementation: 14.8%) and decreased 30-day mortality for hemorrhagic (before implementation: 38.3%; after implementation: 34.4%) and ischemic stroke (before implementation: 16.3%; after implementation: 15.7%). The system’s implementation was also associated with marked increases in the proportion of patients who received neuroimaging, thrombolytic therapy, care in a stroke unit and antithrombotic therapy. Interpretation: The implementation of an organized system of stroke care delivery was associated with improved processes of care and outcomes after stroke.
Evolution of the IS6110-Based Restriction Fragment Length Polymorphism Pattern during the Transmission of Mycobacterium tuberculosis

ABSTRACT Interpretation of the molecular epidemiological data of Mycobacterium tuberculosis is dependent on the validity of the assumptions that have been made. It is assumed that the IS6110 banding pattern is sufficiently stable to define epidemiological events representing ongoing transmission. However, molecular epidemiological data also support the observation that the IS6110 banding pattern may change over time. Factors affecting this rate may include the nature and duration of disease in a host and the opportunity to experience different host environments during the transmission cycle. To estimate the rate of IS6110 change occurring during the process of transmission, M. tuberculosis isolates from epidemiologically linked patients were genotypically characterized by restriction fragment length polymorphism (RFLP) analysis. The identification of IS6110 banding pattern changes during ongoing transmission suggested that a rate could be estimated. IS6110 change was significantly associated with strains with >5 IS6110 elements (P = 0.013) and was not observed in low-copy-number isolates. The minimum rate of appearance of variant strains was calculated to be 0.14 variant cases per source-case per year. This data suggest that clustering of isolates based on identical RFLP patterns is expected to underestimate transmission in patients infected with high-copy-number isolates. A model based on the rate of appearance of both variant and invariant strains demonstrates that the genotypically defined population structure may change by 18.6% during the study period of approximately 6.5 years. The implications for the use of RFLP data for epidemiologic study are discussed.
Electrical Test Structures for the Characterization of Optical Proximity Correction

Resistive electrical test structures have been designed to enable the characterization of optical proximity correction (OPC) applied to a right-angled corner in a conducting track. The OPC consists of square serifs that are either added to the outside corner or subtracted from the inner corner. Varying degrees of OPC can be applied by changing the size of the square serif or by changing the amount by which it encroaches on or protrudes from the corner. A prototype test mask has been fabricated that contains test structures suitable for on-mask electrical measurement. The same mask was used to print the test pattern in polysilicon and aluminium using an i-line lithography tool and results from these structures clearly show that OPC has an impact on the resistance of the final printed features. In particular, the level of corner rounding is dependent upon the dimensions of the serifs employed and the measured resistance can be used to characterize the effects of different levels of OPC applied to the inner corners.