Miracle-dz/UniFAR-FTUs huggingface dataset:
Collagen crosslinking in the management of advanced non-resolving microbial keratitis

Aim To evaluate the efficacy and safety of corneal collagen crosslinking (CXL) in the management of culture proven microbial keratitis. Methods 15 eyes of 15 patients of microbial keratitis were included in the study. Nine patients had bacterial keratitis and six had fungal keratitis. All patients underwent microbiological evaluation to identify the causative organism. The depth of the infiltrate was determined clinically with slit lamp and measured manually using anterior segment optical coherence tomography. Patients were treated with antibiotics/antifungals and those who did not respond to at least 2 weeks of topical medications underwent CXL as per the standard protocol. The same preoperative topical medications were continued post-CXL. All patients were followed up every third day and observed for signs of resolution of microbial keratitis. Results Six of nine patients with bacterial keratitis and three of six patients with fungal keratitis resolved following CXL treatment. Patients with deep stromal keratitis or endothelial plaque failed to resolve. All patients had resolution of pain on the first postoperative day. There was an appearance of or increase in hypopyon in seven patients. No intraoperative or postoperative complications were noticed. Conclusions CXL appears to be an effective procedure in the management of superficial microbial keratitis. It can be used as an adjunctive treatment in the management of non-resolving microbial keratitis.
Balancing the risks and benefits of biologic therapy in inflammatory bowel diseases

Introduction: The incidence of Inflammatory Bowel Diseases (IBD) is rising and overall epidemiology is changing. Goals of IBD therapy are also fast changing to reflect the concept of mucosal healing. IBD management is increasingly revolving around questions of ideal positioning of biologic therapies. Areas covered: This paper covers important concepts regarding two classes of biologic medications approved for treatment of IBD in the United States – anti-TNF-α agents and lymphocyte-homing antagonists. Topics covered include drug mechanism of action, pharmacokinetic considerations for the clinician including therapeutic drug monitoring, summary of current evidence of drug efficacy in IBD focusing on randomized, controlled trial data. Additionally, nuanced discussion of medication side-effects and adverse reactions is presented. Expert opinion: Paradigms of treatment goals in IBD are changing with increasing focus on mucosal healing. Concomitantly, our understanding of important factors that impact drug pharmacokinetic/pharmacodynamics relationships with biologic agents has increased which will help eventually develop personalized algorithms to optimize the efficacy of these agents. Though direct head-to-head comparisons between these agents are lacking, biologic agents can be considered the safest and most effective therapies introduced for IBD.
Recent Trends in the Prevalence of Chronic Obstructive Pulmonary Disease in Korea

Chronic obstructive pulmonary disease (COPD) had been considered the only major disease that is continuing to increase in prevalence. There were a few studies about the change of the prevalence of COPD, which showed the prevalence of COPD did not increase. In this review, we report on the trends in the prevalence of COPD in Korea using the data from Korea National Health and Nutrition Examination Survey (KNHANES). The prevalence of COPD in 2015 was 13.4% (male, 21.6%; female, 5.8%). The prevalence of COPD did not change much, which ranged from 13.1% to 14.6% during the period from 2010 to 2015. Among the subjects found to have COPD by spirometry, only 2.8% had been diagnosed as COPD by physicians during the period from 2011 and 2015. In conclusion, the prevalence of COPD did not change significantly during the period from 2010 to 2015. And most COPD patients still had not been diagnosed by physicians and consequently had not been treated appropriately.
In vivo and in vitro studies of major surface loop deletion mutants of the Escherichia coli K‐12 maltoporin: contribution to maltose and maltooligosaccharide transport and binding

The trimeric protein LamB of Escherichia coli K‐12 (maltoporin) specifically facilitates the diffusion of maltose and maltooligosaccharides through the outer membrane. Each monomer consists of an 18‐stranded antiparallel β‐barrel with nine surface loops (L1 to L9). The effects on transport and binding of the deletion of some of the surface loops or of combinations of several of them were studied in vivo and in vitro. In vivo, single‐, ΔL4, ΔL5, ΔL6, and double‐loop deletions, ΔL4 + ΔL5 and ΔL5 + ΔL6, abolished maltoporin functions, but not the double deletion ΔL4 + ΔL6 and the triple deletion ΔL4 + ΔL5 + ΔL6. While deletion of the central variable portion of loop L9 (ΔL9v) affected maltoporin function only moderately, the combination of ΔL9v with the double deletion of loops L4 and L6 (triple deletion ΔL4 + ΔL6 + ΔL9v) strongly impaired maltoporin function and resulted in sensitivity to large hydrophilic antibiotics without change in channel size as measured in vitro. In vitro, the carbohydrate‐binding properties of the different loop mutants were studied in titration experiments using the asymmetric and symmetric addition of the mutant porins and of the carbohydrates to one or both sides of the lipid bilayer membranes. The deletion of loop L9v alone (LamBΔL9v), of two loops L4 and L6 (LamBΔL4 +ΔL6), of three loops L4, L5 and L6 (LamBΔL4 +ΔL5 + ΔL6) or of L4, L6 and L9v (LamBΔL4 + ΔL6 +ΔL9v) had relatively little influence on the carbohydrate‐binding properties of the mutant channels, and they had approximately similar binding properties for carbohydrate addition to both sides compared with only one side. The deletion of one of the loops L4 (LamBΔL4) or L6 (LamBΔL6) resulted in an asymmetric carbohydrate binding. The in vivo and in vitro results, together with those of the purification across the starch column, suggest that maltooligosaccharides enter the LamB channel from the cell surface side with the non‐reducing end in advance. The absence of some of the loops leads to obstruction of the channel from the outside, which results in a considerable difference in the on‐rate of carbohydrate binding from the extracellular side compared with that from the periplasmic side.
Antibacterial Activity of Ciprofloxacin-Encapsulated Cockle Shells Calcium Carbonate (Aragonite) Nanoparticles and Its Biocompatability in Macrophage J774A.1

The use of nanoparticle delivery systems to enhance intracellular penetration of antibiotics and their retention time is becoming popular. The challenge, however, is that the interaction of nanoparticles with biological systems at the cellular level must be established prior to biomedical applications. Ciprofloxacin–cockle shells-derived calcium carbonate (aragonite) nanoparticles (C-CSCCAN) were developed and characterized. Antibacterial activity was determined using a modified disc diffusion protocol on Salmonella Typhimurium (S. Typhimurium). Biocompatibilittes with macrophage were evaluated using the 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and 5-Bromo-2′-deoxyuridine (BrdU) assays. Transcriptional regulation of interleukin 1 beta (IL-1β) was determined using reverse transcriptase-polymerase chain reaction (RT-PCR). C-CSCCAN were spherical in shape, with particle sizes ranging from 11.93 to 22.12 nm. Encapsulation efficiency (EE) and loading content (LC) were 99.5% and 5.9%, respectively, with negative ζ potential. X-ray diffraction patterns revealed strong crystallizations and purity in the formulations. The mean diameter of inhibition zone was 18.6 ± 0.5 mm, which was better than ciprofloxacin alone (11.7 ± 0.9 mm). Study of biocompatability established the cytocompatability of the delivery system without upregulation of IL-1β. The results indicated that ciprofloxacin–nanoparticles enhanced the antibacterial efficacy of the antibiotic, and could act as a suitable delivery system against intracellular infections.
Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula

Filamentous cyanobacteria of the genus Lyngbya are important contributors to coral reef ecosystems, occasionally forming dominant cover and impacting the health of many other co-occurring organisms. Moreover, they are extraordinarily rich sources of bioactive secondary metabolites, with 35% of all reported cyanobacterial natural products deriving from this single pantropical genus. However, the true natural product potential and life strategies of Lyngbya strains are poorly understood because of phylogenetic ambiguity, lack of genomic information, and their close associations with heterotrophic bacteria and other cyanobacteria. To gauge the natural product potential of Lyngbya and gain insights into potential microbial interactions, we sequenced the genome of Lyngbya majuscula 3L, a Caribbean strain that produces the tubulin polymerization inhibitor curacin A and the molluscicide barbamide, using a combination of Sanger and 454 sequencing approaches. Whereas ∼293,000 nucleotides of the draft genome are putatively dedicated to secondary metabolism, this is far too few to encode a large suite of Lyngbya metabolites, suggesting Lyngbya metabolites are strain specific and may be useful in species delineation. Our analysis revealed a complex gene regulatory network, including a large number of sigma factors and other regulatory proteins, indicating an enhanced ability for environmental adaptation or microbial associations. Although Lyngbya species are reported to fix nitrogen, nitrogenase genes were not found in the genome or by PCR of genomic DNA. Subsequent growth experiments confirmed that L. majuscula 3L is unable to fix atmospheric nitrogen. These unanticipated life history characteristics challenge current views of the genus Lyngbya.
Assessment of bone marrow involvement in patients with lymphoma: report on a consensus meeting of the Korean Society of Hematology Lymphoma Working Party

In September 2011, the Korean Society of Hematology Lymphoma Working Party held a nationwide conference to establish a consensus for assessing bone marrow (BM) involvement in patients with lymphoma. At this conference, many clinicians, hematopathologists, and diagnostic hematologists discussed various topics for a uniform consensus in the evaluation process to determine whether the BM is involved. Now that the discussion has matured sufficiently to be published, we herein describe the consensus reached and limitations in current methods for assessing BM involvement in patients with lymphoma.
Local extraction of base and thermal resistance of bipolar transistors

We extend the category of parameter extraction methods that utilize weak avalanche under fixed emitter current conditions to extract base resistance. Our new method consistently accounts for self-heating and Early effect so as to arrive at an accurate extraction of both base and thermal resistance. It involves only small variations in bias and temperature conditions, so that parameter extraction as a function of bias and temperature is enabled. The method is directly applicable to transistors - no dedicated test structures are needed - so that the method is cost effective. The method is demonstrated on RF SiGe HBTs.
Specific roles of 5′ RNA secondary structures in stabilizing transcripts in chloroplasts

RNA secondary structures, e.g. stem–loops that are often found at the 5′ and 3′ ends of mRNAs, are in many cases known to be crucial for transcript stability but their role in prolonging the lifetime of transcripts remains elusive. In this study we show for an essential RNA-stabilizing stem–loop at the 5′ end of rbcL gene transcripts in Chlamydomonas that it neither prevents ribonucleases from binding to the RNA nor impedes their movement along the RNA strand. The stem–loop has a formative function in that it mediates folding of a short sequence around its base into a specific RNA conformation, consisting of a helical and single-stranded region, i.e. the real structure required for longevity of rbcL transcripts in chloroplasts. Disturbing this structure renders transcripts completely unstable, even if the sequence of this element is not altered. The requirement of a specific 5′ sequence and structure for RNA longevity suggests an interaction of this element with a trans-acting factor that protects transcripts from rapid degradation in chloroplasts.
Identifying Provider Prejudice in Healthcare

We use simple economic insights to develop a framework for distinguishing between prejudice and statistical discrimination using observational data. We focus our inquiry on the enormous literature in healthcare where treatment disparities by race and gender are not explained by access, preferences, or severity. But treatment disparities, by themselves, cannot distinguish between two competing views of provider behavior. Physicians may consciously or unconsciously withhold treatment from minority groups despite similar benefits (prejudice) or because race and gender are associated with lower benefit from treatment (statistical discrimination). We demonstrate that these two views can only be distinguished using data on patient outcomes: for patients with the same propensity to be treated, prejudice implies a higher return from treatment for treated minorities, while statistical discrimination implies that returns are equalized. Using data on heart attack treatments, we do not find empirical support for prejudice-based explanations. Despite receiving less treatment, women and blacks receive slightly lower benefits from treatment, perhaps due to higher stroke risk, delays in seeking care, and providers over-treating minorities due to equity and liability concerns.
Arsenic in rice and diets of children

Levels of arsenic in Australian and imported rice (n = 36) were evaluated using inductively coupled plasma mass spectrometry (ICP-MS) for total arsenic and a hyphenated high-performance liquid chromatography ICP-MS system for arsenic species. The study also assessed the daily intake of total As from diets of healthy children (n = 15), collected over three consecutive days. A wide variation of total As levels (range: <0.05–0.42 mg/kg) in Australian and imported rice was found. The mean level of total As (0.24 ± 0.09 mg/kg, n = 10) in the Australian rice was relatively higher than imported rice from other countries (0.09 ± 0.04 mg/kg, n = 26). The mean level (0.25 ± 0.08 mg/kg, n = 7) of dimethylarsenic acid was considerably higher than that of inorganic As (III) (0.07 ± 0.03 mg/kg, n = 7) in the Australian rice. Children’s daily intakes of total As varied widely, ranging from 1.7 to 31.2 (11.5 ± 8.9 µg/day), which was comparable to other countries.
Fuzzy risk analysis based on a geometric ranking method for generalized trapezoidal fuzzy numbers

In this study, we present a new method for ranking generalized trapezoidal fuzzy numbers based on the incenter and inradius of a triangle. The proposed method is simple and easy to apply to real life problems. The method can also rank crisp numbers and fuzzy numbers with the same centroid point. Some comparative examples are also given to illustrate the advantages of the proposed method. Based on the proposed ranking method, we also give an application to the fuzzy risk analysis problem.
CD24 is a new oncogene, early at the multistep process of colorectal cancer carcinogenesis.

BACKGROUND & AIMS The aim of this study was to identify genes that play a role in colorectal cancer (CRC) carcinogenesis by analysis of differential gene expression of normal and transformed CRC cell lines. METHODS Gene expression array analysis ([RG-U34] GeneChip) was performed in normal and transformed rat intestinal epithelial cells before and after exposures to celecoxib. In particular, we were looking for (1) altered gene expression in the transformed cells that reverts to normal following exposure to a selective cyclooxygenase-2 inhibitor, (2) novel genes, and (3) genes encoding membrane receptors or ligands. As a validation of the results and for human patients, immunohistochemistry was performed on 398 biological samples from the gastrointestinal tract (normal, polyps, and adenocarcinomas). Human cancer cell lines were tested for their response to anti-CD24 monoclonal antibodies. RESULTS A total of 1081 genes were differently expressed following malignant transformation; 71 genes showed altered expression that reverted to normal following treatment with celecoxib, including the CD24 gene. Immunohistochemistry confirmed that increased expression of CD24 is an early event in CRC carcinogenesis. It was expressed in 90.7% of adenomas and 86.3% of CRCs. Very low expression was seen in normal epithelium (16.6%). Human cancer cell lines showed growth inhibition in response to the antibodies, according to their expression levels of CD24 and in dose- and time-dependent manners. These results were repetitive for 3 different antibodies. CONCLUSIONS CD24 is overexpressed in the colonic mucosa, already at an early stage of carcinogenesis. It may be a useful target for early detection and in CRC therapy.
Postoperative Delirium in the Elderly

Postoperative delirium is common in the elderly in the postoperative period. It can result in increased morbidity, delayed functional recovery, and prolonged hospital stay. In surgical patients, factors such as age, alcohol abuse, low baseline cognition, severe metabolic derangement, hypoxia, hypotension, and type of surgery appear to contribute to postoperative delirium. Anesthetics, notably anticholinergic drugs and benzodiazepines, increase the risk for delirium. Despite the above recommendations, postoperative delirium in the elderly is poorly understood. Clearly, further studies are needed to determine the risk and long-term outcome of delirium in the elderly population. Research is also needed to define the effects of hypoxemia on cerebral function and whether oxygen therapy has any benefits. The geriatric-anesthesiologic intervention program of pre- and postoperative geriatric assessment, early surgery, thrombosis prophylaxis, oxygen therapy, prevention and treatment of perioperative decrease in blood pressure, and vigorous treatment of any postoperative complications showed some promise, but further definitive studies are needed.
The genetic architecture of zinc and iron content in maize grains as revealed by QTL mapping and meta-analysis

Micronutrient malnutrition, especially zinc (Zn) and iron (Fe) deficiency in diets, has aroused worldwide attention. Biofortification of food crops has been considered as a promising approach for alleviating this deficiency. Quantitative trait locus (QTL) analysis was performed to dissect the genetic mechanism of Zn and Fe content in maize grains using a total of 218 F2:3 families derived from a cross between inbred lines 178 and P53. Meta-analysis was used to integrate genetic maps and detect Meta-QTL (MQTL) across several independent QTL researches for traits related to Zn or Fe content. Five significant QTLs and 10 MQTLs were detected. Two informative genomic regions, bins 2.07 and 2.08, showed a great importance for Zn and Fe content QTLs. The correlation between Zn and Fe level in maize grains was proposed by MQTLs as 8 of the 10 involved both traits. The results of this study suggest that QTL mapping and meta-analysis is an effective approach to understand the genetic basis of Zn and Fe accumulation in maize grains.
Apigenin inhibits allergen-induced airway inflammation and switches immune response in a murine model of asthma

Many flavonoids were demonstrated to posses the antiallergic effect. Here we detected whether apigenin, a flavonoid, can attenuate allergen-induced airway inflammation and what is the possible mechanism in a murine model of asthma. Apigenin decreased the degree of the inflammatory cell infiltration, airway hyperresponsiveness, and total immunoglobulin E levels compared with the ovalbumin group. In addition, apigenin triggered the switching of the immune response to allergens toward a T-helper type 1 (Th1) profile. Our data clearly demonstrated that apigenin exhibits an anti-inflammatory activity in a murine asthma model, and can switch the immune response to allergens toward the Th1 profile.
Intraventricular Hemorrhage and Platelet Indices in Extremely Premature Neonates

Intraventricular hemorrhage (IVH) is a multifactorial disorder, the most important risk factors of which are prematurity and low birth weight. Disturbances in cerebral blood flow, inherent fragility of the germinal matrix vasculature, and platelet/coagulation disturbances are the 3 major pathogenic mechanisms. In this context, we investigated the role of platelet indices and several maternal and neonatal characteristics in the development of IVH through a retrospective cohort analysis of 130 extremely premature neonates, 24% of whom presented with severe IVH. There was a significant difference in platelet counts between the IVH and the control group on the first day of life (P=0.046). Presence of IVH was linked with lower birth weight (P=0.006) and lower gestational age (P=0.001). Platelet count on the first day of life was positively correlated with survival (P=0.001) and, along with platelet mass, was indicative of the worst IVH grade recorded for each neonate (P=0.002 and 0.007, respectively). Prolonged prothrombin time was also correlated with IVH (P<0.001), but factor analysis supported no prominent role. Maternal medications seem to play a minor role as well. In conclusion, IVH in extremely premature infants cannot be solely explained by platelet parameters, and further studies are required to determine the relationships between IVH, platelet indices, and outcomes.
Rho-associated kinase-dependent contraction of stress fibres and the organization of focal adhesions

Stress fibres and associated focal adhesions in cells constitute a contractile apparatus that regulates cell motility and contraction. Rho-kinase, an effector molecule of small GTPases, regulates non-muscle cell motility and contractility. Rho-kinase mediates the contraction of stress fibres in a Ca2+-independent manner, and is responsible for slower and more finely tuned contraction of stress fibres than that regulated by myosin light chain kinase activity in living cells. The specific inhibition of the Rho-kinase activity causes cells to not only lose their stress fibres and focal adhesions, but also to appear to lose their cytoplasmic tension. Activated Rho-kinase is also involved in the organization of newly formed stress fibres and focal adhesions in living cells.
Generating Sentences Using a Dynamic

We introduce the Attentive Unsupervised Text (W)riter (AUTR), which is a word level generative model for natural language. It uses a recurrent neural network with a dynamic attention and canvas memory mechanism to iteratively construct sentences. By viewing the state of the memory at intermediate stages and where the model is placing its attention, we gain insight into how it constructs sentences. We demonstrate that AUTR learns a meaningful latent representation for each sentence, and achieves competitive log-likelihood lower bounds whilst being computationally efficient. It is effective at generating and reconstructing sentences, as well as imputing missing words.