Miracle-dz/UniFAR-FTUs huggingface dataset:
Surveillance after endoscopic mucosal resection or endoscopic submucosal dissection for esophageal squamous cell carcinoma

The objectives of surveillance after endoscopic mucosal resection (EMR) or endoscopic submucosal dissection (ESD) for esophageal squamous cell carcinoma are: (i) early detection and treatment of recurrence; and (ii) early detection and treatment of metachronous esophageal squamous cell carcinoma and second primary cancers. Protocols for follow up after EMR or ESD for esophageal squamous cell carcinoma should be based on the risks of lymph node metastasis and distant metastasis as assessed on the basis of tumor staging at initial treatment. Early detection of recurrence or metachronous carcinomas often allows curative or less invasive treatment. Particular attention should be paid to the development of metachronous esophageal squamous cell carcinomas and second primary cancers (in particular, head and neck cancer and gastric cancer because of their high incidence).
The fluorescence and infrared absorption probe para‐cyanophenylalanine: Effect of labeling on the behavior of different membrane‐interacting peptides

Total syntheses and complete characterizations of singly substituted PheCN‐based analogs of alamethicin AlaP, which is active on model and natural membranes, and the TM peptide, which inserts in a transmembrane orientation in lipid bilayers, are reported. The syntheses of the AlaP analogs were performed in solution, while those of TM and its analogs were carried out by solid phase. Using the cyanophenyl fluorescence and infrared (IR) absorption probe, an in‐depth investigation of the self‐association, membrane‐interacting, permeabilizing, and orientation properties of these peptides were conducted. The aromatic residue incorporated induces only a negligible modification to the properties of the parent peptides. The PheCN IR absorption band was located between 2228 and 2230 cm−1 for all peptides, irrespective of the position of labeling. By contrast, as the width of this band varied significantly with the depth of probe insertion in the bilayer, it could represent a good marker of the PheCN position in phospholipid membranes. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 521–532, 2015.
The effect of three different visual monitoring strategies on the accuracy of leg‐before‐wicket decisions by cricket umpires

Background: Leg‐before‐wicket (LBW) dismissals in cricket require exacting visual judgements by umpires, a task complicated by the requirement to also adjudicate on where the bowler's front foot is relative to the popping crease line about the time the ball leaves the bowler's hand. The umpire must then judge as soon as possible afterwards whether the direction of the flight of the ball is in line with the batsman's stumps. This study investigated whether the accuracy of cricket umpires' decision‐making in leg‐before‐wicket dismissals is affected by varying the method by which umpires monitor bowlers' feet at the point of delivery of the ball.
A comparison of four different conformations adopted by human telomeric G‐quadruplex using computer simulations

The telomeric G‐quadruplexes for their unique structural features are considered as potential anticancer drug targets. These, however, exhibit structural polymorphism as different topology types for the intra‐molecular G‐quadruplexes from human telomeric G‐rich sequences have been reported based on NMR spectroscopy and X‐ray crystallography. These techniques provide detailed atomic‐level information about the molecule but relative conformational stability of the different topologies remains unsolved. Therefore, to understand the conformational preference, we have carried out quantum chemical calculations on G‐quartets; used all‐atom molecular dynamics (MD) simulations and steered molecular dynamics (SMD) simulations to characterize the four human telomeric G‐quadruplex topologies based on its G‐tetrad core‐types, viz., parallel, anti‐parallel, mixed‐(3 + 1)‐form1 and mixed‐(3 + 1)‐form2. We have also studied a non‐telomeric sequence along with these telomeric forms giving a comparison between the two G‐rich forms. The structural properties such as base pairing, stacking geometry and backbone conformations have been analyzed. The quantum calculations indicate that presence of a sodium ion inside the G‐tetrad plane or two potassium ions on both sides of the plane give it an overall planarity which is much needed for good stacking to form a helix. MD simulations indicate that capping of the G‐tetrad core by the TTA loops keep the terminal guanine bases away from water. The SMD simulations along with equilibrium MD studies indicate that the parallel and non‐telomeric forms are comparatively less stable. We could come to the conclusion that the anti‐parallel form and also the mixed‐(3 + 1)‐form1 topology are most likely to represent the major conformation. , 2016. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 83–99, 2016
Sensory ocular dominance based on resolution acuity, contrast sensitivity and alignment sensitivity

Background: Ocular dominance is the superiority or preference of one eye over the other in terms of sighting, sensory function (for example, visual acuity) or persistence in binocular rivalry. There is poor agreement between sighting and sensory dominance and findings are equivocal on the possible neural basis of ocular dominance and its significance. Thus, there are questions on the meaning and importance of ocular dominance. Despite the lack of clarity in this area, ocular dominance is used clinically, for example, as the basis for decisions on monovision in contact lens wear and on treatment of anomalies of binocular vision.
New directions for protease inhibitors directed drug discovery

Proteases play crucial roles in various biological processes, and their activities are essential for all living organisms—from viruses to humans. Since their functions are closely associated with many pathogenic mechanisms, their inhibitors or activators are important molecular targets for developing treatments for various diseases. Here, we describe drugs/drug candidates that target proteases, such as malarial plasmepsins, β‐secretase, virus proteases, and dipeptidyl peptidase‐4. Previously, we reported inhibitors of aspartic proteases, such as renin, human immunodeficiency virus type 1 protease, human T‐lymphotropic virus type I protease, plasmepsins, and β‐secretase, as drug candidates for hypertension, adult T‐cell leukaemia, human T‐lymphotropic virus type I‐associated myelopathy, malaria, and Alzheimer's disease. Our inhibitors are also described in this review article as examples of drugs that target proteases. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 563–579, 2016.
Ocular preference following implantation of aspheric and spherical intraocular lenses; an intra‐individual comparison

Purpose: Recently, intraocular lenses (IOLs) that possess an aspheric design, compensating for the spherical aberration (SA) of the cornea, have been developed. We designed this study to compare a group of patients who had undergone bilateral cataract surgery and had received one spherical IOL and one aspheric IOL, to assess their ocular preference.
Comparison of SHF and SSF processes from steam‐exploded wheat straw for ethanol production by xylose‐fermenting and robust glucose‐fermenting Saccharomyces cerevisiae strains

In this study, bioethanol production from steam‐exploded wheat straw using different process configurations was evaluated using two Saccharomyces cerevisiae strains, F12 and Red Star. The strain F12 has been engineerically modified to allow xylose consumption as cereal straw contain considerable amounts of pentoses. Red Star is a robust hexose‐fermenting strain used for industrial fuel ethanol fermentations and it was used for comparative purposes. The highest ethanol concentration, 23.7 g/L, was reached using the whole slurry (10%, w/v) and the recombinant strain (F12) in an SSF process, it showed an ethanol yield on consumed sugars of 0.43 g/g and a volumetric ethanol productivity of 0.7 g/L h for the first 3 h. Ethanol concentrations obtained in SSF processes were in all cases higher than those from SHF at the same conditions. Furthermore, using the whole slurry, final ethanol concentration was improved in all tests due to the increase of potential fermentable sugars in the fermentation broth. Inhibitory compounds present in the pretreated wheat straw caused a significantly negative effect on the fermentation rate. However, it was found that the inhibitors furfural and HMF were completely metabolized by the yeast during SSF by metabolic redox reactions. An often encountered problem during xylose fermentation is considerable xylitol production that occurs due to metabolic redox imbalance. However, in our work this redox imbalance was counteracted by the detoxification reactions and no xylitol was produced. Biotechnol. Bioeng. 2008;100: 1122–1131. © 2008 Wiley Periodicals, Inc.
Evaluation of retinal nerve fibre layer thickness and visual evoked potentials in optic neuritis associated with multiple sclerosis

Background: The aim was to compare the retinal nerve fibre layer (RNFL) thickness and visual evoked potentials (VEP) among eyes with multiple sclerosis (MS)‐associated optic neuritis, unaffected eyes of the same patients and eyes of disease‐free controls. Changes in RNFL thickness, visual acuity (VA) and VEP over time are evaluated in MS‐associated optic neuritis.
Epidermal growth factor promotes breast cancer cell chemotaxis in CXCL12 gradients

The chemokine receptor CXCR4 and its ligand CXCL12 play an important role in breast cancer invasion and metastasis, and induce the chemotaxis of various types of cancer cells. Previous studies of CXCL12‐induced chemotaxis have, for the most part, relied on endpoint assays (e.g., transwell assays) that provide poor control over the cell microenvironment. Specifically, these assays lacked the ability to dissect the role that autocrine and paracrine growth factors play in chemokine‐induced cancer cell chemotaxis. Here, we employ a microfluidic chemotaxis chamber that allows the effects of specific exogenous factors on cell migration to be directly characterized, without the interference of autocrine/paracrine signaling. Using this approach, we investigated the migration of MDA‐MB‐231 breast cancer cells in well‐defined CXCL12 gradients. We found that CXCL12 alone failed to stimulate chemotaxis of these cells; however, when the CXCL12 gradient was supplemented with a uniform stimulus of either EGF or conditioned media, a directional response was induced. This dependence on growth factor signaling points to the importance of autocrine and paracrine factors in determining the migratory response of the cells, and may play an important role in cancer metastasis. Biotechnol. Bioeng. 2008;100: 1205–1213. © 2008 Wiley Periodicals, Inc.
Generation of baculovirus vectors for the high‐throughput production of proteins in insect cells

The baculovirus expression system is one of the most popular methods used for the production of recombinant proteins but has several complex steps which have proved inherently difficult to adapt to a multi‐parallel process. We have developed a bacmid vector that does not require any form of selection pressure to separate recombinant virus from non‐recombinant parental virus. The method relies on homologous recombination in insect cells between a transfer vector containing a gene to be expressed and a replication‐deficient bacmid. The target gene replaces a bacterial replicon at the polyhedrin loci, simultaneously restoring a virus gene essential for replication. Therefore, only recombinant virus can replicate facilitating the rapid production of multiple recombinant viruses on automated platforms in a one‐step procedure. Using this vector allowed us to automate the generation of multiple recombinant viruses with a robotic liquid handler and then rapidly screen infected insect cell supernatant for the presence of secreted proteins. Biotechnol. Bioeng. © 2008 Wiley Periodicals, Inc.
Food Variety and Dietary Diversity as Indicators of the Dietary Adequacy and Health Status of an Elderly Population in Sharpeville, South Africa

ABSTRACT This cross-sectional, analytical study was a comprehensive health assessment focusing on dietary quality of 170 randomly selected elderly respondents in Sharpeville, South Africa. The methods included a sociodemographic, health food frequency questionnaire, 24 h-recall questionnaires, and anthropometric and biochemical measurements. The low mean±standard deviation (SD) dietary diversity score (3.41±1.34) and food variety score (4.77±2.2) compared with poverty parameters confirmed household food insecurity in this community. Although three (n = 99, 58.6%) or two (n = 49, 28.9%) daily meals were mostly consumed, these were mainly carbohydrate-based and nutrient-deficient. The cereal group (2.01±0.81) had the highest mean food variety score ±SD, followed by dairy (0.62±0.53) and flesh foods (0.40±0.53). When a mean adequacy ratio of 70% was used as a cut-off point for nutrient adequacy, it was found that the food variety score must be eight or higher and the dietary variety score must be at least six. These indicators thus have a high ability to identify those respondents with an inadequate diet but lower ability to identify those respondents with a nutritionally adequate diet. The data further showed a trend that with a higher food variety and dietary diversity, a better mean adequacy ratio is reached for this low-income group of elderly subjects. In conclusion, the results showed that food variety and dietary diversity scores give a fairly good assessment of the adequacy of the diet, and scoring dietary diversity is a significant, yet simple tool to identify elderly persons at risk of food and nutrition insecurity.
Modeling fluid flow through irregular scaffolds for perfusion bioreactors

Direct perfusion of 3D tissue engineered constructs is known to enhance osteogenesis, which can be partly attributed to enhanced nutrient and waste transport. In addition flow mediated shear stresses are known to upregulate osteogenic differentiation and mineralization. A quantification of the hydrodynamic environment is therefore crucial to interpret and compare results of in vitro bioreactor experiments. This study aims to deal with the pitfalls of numerical model preparation of highly complex 3D bone scaffold structures and aims to provide more accurate wall shear stress (WSS) estimates. µCT imaging techniques were used to reconstruct the geometry of both a titanium (Ti) and a hydroxyapatite scaffold, starting from 430 images with a resolution of 8 µm. To tackle the tradeoff between model size and mesh resolution we selected two concentric regions of interest (cubes with a volume of 1 and 3.375 mm3, respectively) for both scaffolds. A flow guidance in front of the real inlet surface of the scaffold was designed to mimic realistic inlet conditions. With a flow rate of 0.04 mL/min perfused through a 5 mm diameter scaffold at an inlet velocity of 33.95 µm/s we obtained average WSSs of 1.10 and 1.46 mPa for the 1 mm3 and the 3.375 mm3 model of the hydroxyapatite scaffold compared to 1.40 and 1.95 mPa for the 1 mm3 model and the 3.375 mm3 model of the Ti scaffold, showing the important influence of the scaffold micro‐architecture heterogeneity and the proximity of boundaries. To assess that influence we selected cubic portions, of which the WSS data were analyzed, with the same size and the same location within both 1 and 3.375 mm3 cubic models. Varying the size of the inner portions simultaneously in both model selections gives a quantification of the sensitivity to boundary neighborhood. This methodology allows to get more insight in the complex concept of tissue engineering and will likely help to understand and eventually improve the fluid‐mechanical aspects. Biotechnol. Bioeng. 2009;103: 621–630. © 2009 Wiley Periodicals, Inc.
Prion protein self-interaction in prion disease therapy approaches

Transmissible spongiform encephalopathies (TSEs) or prion diseases are unique disorders that are not caused by infectious micro-organisms (bacteria or fungi), viruses or parasites, but rather seem to be the result of an infectious protein. TSEs are comprised of fatal neurodegenerative disorders affecting both human and animals. Prion diseases cause sponge-like degeneration of neuronal tissue and include (among others) Creutzfeldt–Jacob disease in humans, bovine spongiform encephalopathy (BSE) in cattle and scrapie in sheep. TSEs are characterized by the formation and accumulation of transmissible (infectious) disease-associated protease-resistant prion protein (PrPSc), mainly in tissues of the central nervous system. The exact molecular processes behind the conversion of PrPC into PrPSc are not clearly understood. Correlations between prion protein polymorphisms and disease have been found, however in what way these polymorphisms influence the conversion processes remains an enigma; is stabilization or destabilization of the prion protein the basis for a higher conversion propensity? Apart from the disease-associated polymorphisms of the prion protein, the molecular processes underlying conversion are not understood. There are some notions as to which regions of the prion protein are involved in refolding of PrPC into PrPSc and where the most drastic structural changes take place. Direct interactions between PrPC molecules and/or PrPSc are likely at the basis of conversion, however which specific amino acid domains are involved and to what extent these domains contribute to conversion resistance/sensitivity of the prion protein or the species barrier is still unknown.
How Safe Is the Operative Treatment of Gartland Type 2 Supracondylar Humerus Fractures in Children?

Whereas operative treatment of supracondylar fractures is now standard of care for Gartland type 3 supracondylar humerus fractures in children, the treatment of type 2 fractures remains somewhat controversial. The purpose of this article was to examine the safety and efficacy of closed reduction and pinning of type 2 supracondylar humerus fractures in children. Methods: We performed a retrospective review of 189 type 2 supracondylar humerus fractures operatively treated at one tertiary care children's hospital from 2000 to 2006. Data were acquired from a review of radiographs and clinical notes. Results: We found no intraoperative surgical or anesthetic complications in our series. None of our cases lost reduction after closed reduction and percutaneous pinning. There were 4 pin tract infections (2.1%) in our series: 3 were treated with antibiotics, and 1 needed irrigation and debridement in the operating room. This was the only patient who required reoperation for any reason. Conclusions: In this study, the largest reported series of type 2 supracondylar humerus fractures in children, we found an extremely low rate of complications after closed reduction and percutaneous pinning; secondary operations were also uncommon (0.5%). Our series demonstrates a high probability of satisfactory outcome after operative treatment of type 2 supracondylar fractures compared with previous studies of children treated by closed reduction without pinning. Level of Evidence: Therapeutic study, level 4 (case series [no or historical control group]).
Qualitative Versus Quantitative Radiographic Analysis of Foot Deformities in Children With Hemiplegic Cerebral Palsy

Background: Qualitative assessments of standing plain radiographs are frequently used to determine treatment strategies and assess outcomes for the management of a wide range of foot and ankle conditions in children. A quantitative technique for such analyses would presumably be more precise and reliable. The goal of this study was to compare qualitative and quantitative techniques for the assessment of plain radiographs of the foot and ankle in children with hemiplegic type cerebral palsy (CP). Methods: Standing anteroposterior and lateral radiographs of the foot and ankle of the involved side for 49 children with hemiplegic CP were analyzed qualitatively by 2 pediatric orthopaedists, based upon a 3-segment (hindfoot, midfoot, and forefoot) foot model. Quantitative assessment of the same radiographs was performed by 2 examiners, using 6 radiographic measurements developed to describe the alignment of the foot based upon the same 3-segment model. Intraobserver and interobserver reliability was determined for both the qualitative and the quantitative techniques. The qualitative and quantitative techniques were compared to determine agreement. Results: The qualitative technique demonstrated poor-to-fair interobserver reliability (percent agreement range, 23%-31%; weighted &kgr; range, 0.291-0.568). The quantitative technique demonstrated good-to-excellent intraobserver (correlation coefficient range, 0.81-0.99) and interobserver (correlation coefficient range, 0.81-0.97) reliability. Percent agreement between the quantitative and the qualitative techniques for the assessment of foot segmental alignment for each examiner ranged from 22.2% to 100% (mean agreement for examiner 1 was 51% [correlation coefficient range, 0.04-0.48]; mean agreement for examiner 2 was 65.3% [correlation coefficient range, 0.22-0.85]). Percent agreement between the quantitative technique and both observers ranged from 11.1% to 83.3% (mean agreement was 36.7% [correlation coefficient range, 0.17-0.94]). Discussion: Reliable quantitative radiographic analysis of the segmental alignment of the involved foot and ankle in children with hemiplegic CP is possible and is more precise and reliable than traditional qualitative techniques. Quantitative techniques can identify a wider range of foot segmental malalignments and should facilitate deformity analysis, preoperative planning, assessment of outcome, and comparison of results between centers.
Correlation of Pediatric Outcomes Data Collection Instrument With Measures of Active Movement in Children With Brachial Plexus Birth Palsy

Background: The purpose of this investigation was to characterize the range of Pediatric Outcomes Data Collection Instrument (PODCI) scores in children with brachial plexus birth palsy (BPBP) and determine its correlation with 3 published measures of active motion and function. Methods: One hundred fifty children with BPBP between the ages of 2 and 10 years were evaluated. Active upper-extremity motion was assessed using the modified Mallet Classification (MC), the Toronto Test score (TTS), and the Hospital for Sick Children Active Movement Scale. At the time of evaluation, patients and/or families were administered the age-appropriate PODCI questionnaire, and PODCI scores were compared with published normative data. Linear regression analysis was used to assess the correlation between MC, TTS, and Active Movement Scale as predictors of PODCI scores. Results: Mean PODCI global function score in the BPBP patients was 82.4 (range, 35.1-100), significantly lower than the published value of 93.3 in healthy, age-matched norms (P < 0.01). The mean upper-extremity subscore was 70.8 versus 92.0 in healthy age-matched controls (P < 0.01). Sports/physical functioning scores averaged 81 points among BPBP patients compared with 90 points in healthy norms (P < 0.01). Mean mobility, comfort/pain, and happiness subscores were also significantly lower than normative values by 5, 7, and 4 points, respectively (P < 0.01). While significant correlations were observed between PODCI scores and all measures of active movement, the modified MC correlated most highly with PODCI global function scores in patients aged 2 to 5 years, whereas the TTSs best correlated with global function in patients aged 6 to 10 years. Conclusion: Brachial plexus birth palsy patients have lower global and upper-extremity function compared with their healthy, age-matched peers, as measured by the PODCI. Physician-derived measures of active movement correlate with the patient/parent-derived PODCI scores and may be used to predict global function, upper-extremity function, and sports/physical activity in children 2 to 10 years of age with BPBP. Level of Evidence: Level I (diagnostic).