Miracle-dz/UniFAR-FTUs huggingface dataset:
Models of Accommodation Deficiency in Presbyopia Patients

Purpose: We describe new phenomenological illumination-dependent static models of the accommodation deficiency for patients with presbyopia. Such models are suitable for vision restoration with adaptive-optics accommodating eyeglasses and contact lenses. Methods: Data from fifteen participants over the age of 45 and diagnosed with presbyopia was collected. Participants were asked to wear a pair of mechanically-tunable eyeglasses and clearly identify the optotypes corresponding to the LogMAR 0.0 line on Early Treatment of Diabetic Retinopathy Study (ETDRS) charts, by suitably adjusting the optical powers of the lenses on these tunable eyeglasses for each measurement. Seven ETDRS charts, placed at distances from the patients varying from 4 m through 30 cm, were used under three chart illumination levels (75 lx, 500 lx and 800 lx). The optical power of the lenses in the patient-adjusted tunable eyeglasses was subsequently measured using a Shack-Hartman wavefront sensor for each chart, which provided the accommodation deficiency data of the participants. Results: The measured accommodation deficiency data from 15 presbyopes was curve-fitted to a model for each patient. The calculated root-mean-square error values for the fitted models ranged between 0.09 D - 0.67 D over a 3.08 D accommodation stimulus range. Conclusions: The data shows that while accommodation deficiency in humans is a function of the stimulus, it is also strongly dependent on the object illumination and age of the patients. The models adequately describe the relation between static accommodation deficiency, accommodation stimulus and object illumination.
Hospital preparedness in epidemics by using simulation. The case of COVID-19

This paper presents a discrete event simulation model to support the decision-making concerned with the short-term planning of the necessary hospital resources, especially Intensive Care Unit (ICU) beds, to face outbreaks, as the SARS-CoV-2. Being used as a short-term forecasting tool, the simulation model requires an accurate representation of the current system state and high fidelity in mimicking the system dynamics from that state. The two main components of the simulation model are the stochastic modeling of the admission of new patients and the patient flow through the hospital facilities. For the patient arrival process, we analyze different models based on growth curves of the twenty most affected countries (until June 15) and propose the use of the Gompertz curve. The length of stay is divided into several stages, each one modeled separately. We analyze the starting of the simulation model, which requires different procedures depending on the information available about the patients currently hospitalized. We also report the use of this simulation model during the COVID-19 outbreak in the Autonomous Community of Navarre, in Spain. Every day, the research team informed the regional logistic team in charge of planning the health resources, who programmed the ward and ICU beds based on the resulting predictions.
Bio-Inspired Attentive Segmentation of Retinal OCT imaging

Albeit optical coherence imaging (OCT) is widely used to assess ophthalmic pathologies, localization of intra-retinal boundaries suffers from erroneous segmentations due to image artifacts or topological abnormalities. Although deep learning-based methods have been effectively applied in OCT imaging, accurate automated layer segmentation remains a challenging task, with the flexibility and precision of most methods being highly constrained. In this paper, we propose a novel method to segment all retinal layers, tailored to the bio-topological OCT geometry. In addition to traditional learning of shift-invariant features, our method learns in selected pixels horizontally and vertically, exploiting the orientation of the extracted features. In this way, the most discriminative retinal features are generated in a robust manner, while long-range pixel dependencies across spatial locations are efficiently captured. To validate the effectiveness and generalisation of our method, we implement three sets of networks based on different backbone models. Results on three independent studies show that our methodology consistently produces more accurate segmentations than state-of-the-art networks, and shows better precision and agreement with ground truth. Thus, our method not only improves segmentation, but also enhances the statistical power of clinical trials with layer thickness change outcomes.
Determinants of Short Birth Intervals among married women in Karachi, Pakistan

Introduction: Birth spacing is a critical pathway to improving reproductive health. The World Health Organization recommends a minimum of 33-month interval between two consecutive births to reduce maternal, perinatal, and infant morbidity and mortality. Our study evaluated factors associated with short birth intervals (SBIs) of less than 33 months between two consecutive births, in three peri-urban municipalities in Karachi, Pakistan. Methods: We used data from a cross-sectional study among married women of reproductive age (MWRA) who had at least one live birth in the six years preceding the survey (N=2394). Information regarding their sociodemographic characteristics, reproductive history, fertility preferences, family planning history, and a six-year reproductive calendar were collected. To identify factors associated with SBIs, we fitted simple and multiple Cox-proportional hazards models and computed hazard ratios (HR) with their 95% confidence intervals (CI). Results: The median birth interval was 25 months (IQR: 14-39 months), with 22.9% of births occurring within 33 months of the index birth. Women increasing age [25-29 years (aHR=0.64, 95% CI: 0.54-0.77), 30+ years (aHR=0.30, 95% CI: 0.23-0.40) compared to <25 years]; secondary education [aHR 0.78. 95% CI: 0.65-0.93], intermediate education [aHR 0.63, 95% CI: 0.49-0.82], higher education (aHR=0.71, 95% CI: 0.53-0.96) compared to no education, and a male child of the index birth (aHR=0.79, 95% CI: 0.68-0.92) reduced the likelihood of SBIs. Women younger age <20 years [aHR 1.32, 95% CI 1.03-1.70] compared to 20-24 years, and those who did not use contraception within 9-months of the index birth had a higher likelihood for SBIs for succeeding birth compared to those who used contraception (aHR=2.33, 95% CI: 2.01-2.70). Conclusion: This study evaluates factors associated with birth spacing practices among married women of childbearing age in urban settlements of Karachi. Our study shows that birth intervals in the study population are lower than the national average. To optimize birth intervals, programs should target child spacing strategies and counsel MWRA on the benefits of optimal birth spacing, family planning services and contraceptive utilization.
Perfusion Chamber for Observing a Liposome-Based Cell Model Prepared by a Water-in-Oil Emulsion Transfer Method

For the construction of a chemical model of contemporary living cells, the so-called water-in-oil emulsion transfer (WOET) method has drawn much attention as one of the promising preparation protocols for cell-sized liposomes encapsulating macromolecules and even micrometer-sized colloidal particles in high yields. Combining the throughput and accuracy of the observation is the key to developing a synthetic approach based on the liposomes prepared by the WOET method. Recent advances in microfluidic technology can provide a solution. By means of surface modification of a poly(dimethylsiloxane)-type microfluidic device integrating size-sorting and trapping modules, here, we enabled a simultaneous direct observation of the liposomes with a narrow size distribution, which were prepared by the WOET method. As a demonstration, we evaluated the variance of encapsulation of polystyrene colloidal particles and water permeability of the cell-sized liposomes prepared by the WOET method in the device. Since the liposomes prepared by the WOET method are useful for constructing cell models with an easy protocol, the current system will lead to a critical development of not only supramolecular chemistry and soft matter physics but also synthetic biology.
Past, Present, and Future of Gastrointestinal Microbiota Research in Cats

The relationship between microbial community and host has profound effects on the health of animals. A balanced gastrointestinal (GI) microbial population provides nutritional and metabolic benefits to its host, regulates the immune system and various signaling molecules, protects the intestine from pathogen invasion, and promotes a healthy intestinal structure and an optimal intestinal function. With the fast development of next-generation sequencing, molecular techniques have become standard tools for microbiota research, having been used to demonstrate the complex intestinal ecosystem. Similarly to other mammals, the vast majority of GI microbiota in cats (over 99%) is composed of the predominant bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Many nutritional and clinical studies have shown that cats’ microbiota can be affected by several different factors including body condition, age, diet, and inflammatory diseases. All these factors have different size effects, and some of these may be very minor, and it is currently unknown how important these are. Further research is needed to determine the functional variations in the microbiome in disease states and in response to environmental and/or dietary modulations. Additionally, further studies are also needed to explain the intricate relationship between GI microbiota and the genetics and immunity of its host. This review summarizes past and present knowledge of the feline GI microbiota and looks into the future possibilities and challenges of the field.
Association of JMJD2B and Hypoxia-Inducible Factor 1 Expressions with Poor Prognosis in Osteosarcoma

Background JMJD2B has been reported to be implicated in malignant tumors. This study is aimed at exploring the expression and prognostic significance of JMJD2B in osteosarcoma and its association with hypoxia-inducible factor 1 (HIF1). Methods The histopathological and clinical characteristics were retrospectively reviewed from 53 osteosarcoma patients. JMJD2B and HIF1 were examined by immunohistochemical staining of paraffin-embedded osteosarcoma samples, and their association with clinical characteristics was examined by Spearman's test. Overall survival was examined by Kaplan-Meier analysis, and prognostic factors were identified by univariate and multivariate regression analyses. Results JMJD2B and HIF1 expression levels were both significantly associated with Enneking stage, distant metastasis, and neoadjuvant chemotherapy, and the JMJD2B and HIF1 expressions were positively correlated (p < 0.001, R = 0.752). In addition, univariate analysis showed that the expression of both JMJD2B and HIF1 was significantly associated with overall survival, but multivariate analysis showed that only JMJD2B expression was significantly associated with overall survival in osteosarcoma patients. Conclusions JMJD2B and HIF1 expression levels show significant correlation with osteosarcoma progression, and JMJD2B could predict poor prognosis of osteosarcoma patients.
Evaluation of Delayed Secondary Enrichment Method for Salmonella Isolation in Feed and Food Manufacturing Plant

To establish an e $ cient method for detection and isolation of Salmonella in feed and food manufacturing plant, we evaluated the delayed secondary enrichment (DSE) method, which has already been acknowledged in the ﬁeld of poultry hygiene. In order to evaluate the detection rate by the increase of pre-enrichment culture and selective enrichment broth, the oilmeal samples ( n A 182) were examined using di # erent volume (10 m l and 90 m l ) of the Hajna-tetrathionate broth (HTT). As a result, the sample with di # erent result was only two (1.1 B ). The detection sensitivities of these 2 methods were same ( p C 0.05). We examined oilseed ( n A 34) and swab samples ( n A 92) of environment in the oilmeal manufacturing plant. The DSE method alone showed the highest rate of Salmonella detection at 14.3 B (18 / 126), followed by the HTT-DHL method and HTT-CHROMagar Salmonella method, both at 12.7 B (16/126). Moreover, O antigen group of isolates detected by the DSE method was di # erent from those of HTT-DHL method in 7 samples. It was found that the detection sensitivity of the DSE method was high. Our ﬁndings suggest that O antigen group of isolates detected by the DSE method may di # er from those of conventional enrichment methods. We conclude that DSE method is a simple and e $ cient method for epidemiological investigations of Salmonella in environments, such as food manufacturing plants.
Effect and Safety of Transcutaneous Auricular Vagus Nerve Stimulation on Recovery of Upper Limb Motor Function in Subacute Ischemic Stroke Patients: A Randomized Pilot Study

Background Transcutaneous auricular vagus nerve stimulation (taVNS) is regarded as a potential method for recovery in stroke. The effectiveness of taVNS in acute and subacute stroke should be further discussed as previously, only a few small-scale trials have focused on chronic stroke patients. The objective of this study is to investigate the effect and safety of taVNS on upper limb motor function in subacute ischemic stroke patients. Methods Twenty-one subacute ischemia stroke patients with single upper limb motor function impairment were enrolled and randomly assigned to conventional rehabilitation training with real or sham taVNS, delivered for 15 consecutive days. Electrodes were fixed to the cymba conchae of the left ear with or without electrical stimulation. Conventional rehabilitation training was performed immediately after the end of real or sham taVNS by the same therapists. Baseline assessments were performed on day 0 of enrollment, and posttreatment evaluations were performed at 15 days, 4 weeks, and 12 weeks after the first intervention. The assessment included the upper limb Fugl-Meyer assessment (FMA-U), the Wolf motor function test (WMFT), the Functional Independence Measurement (FIM), and Brunnstrom stage. Heart rate (HR) and blood pressure (BP) were measured before and after each taVNS intervention. At the same time, any adverse effects were observed during the procedure. Outcomes were assessed by a blind evaluator. Results There were no significant differences in FMA-U, WMFT, FIM, and Brunnstrom scores between the two groups at baseline (P > 0.05). At the endpoint, the FMA-U, WMFT, and FIM scores were significantly higher than before treatment (P < 0.05), and there was a significantly greater improvement of those measurements in taVNS group compared with sham-taVNS group (P < 0.05). Significant improvements in FMA-U score were found between groups at follow-up. Only one case of skin redness occurred during the study. Conclusions This study revealed that taVNS appeared to be beneficial to the recovery of upper limb motor function in subacute ischemia stroke patients without obvious adverse effects. Trial registration. This trial is registered with ChiCTR1800019635 on 20 November 2018 (http://www.chictr.org.cn/showproj.aspx? proj=32961).
Hepatic Polarization Accelerated by Mechanical Compaction Involves HNF4α Activation

There remain few data about the role of homeostatic compaction in hepatic polarization. A previous study has found that mechanical compaction can accelerate hepatocyte polarization; however, the cellular mechanism underlying the effect is mostly unclear. Hepatocyte nuclear factor 4 alpha (HNF4α) is crucial for hepatic polarization in liver morphogenesis. Therefore, we sought to identify any possible involvement of HNF4α in the process of hepatocyte polarization accelerated by mechanical compaction. We first verified in the nonhepatic cell model HEK-293T, and the hepatic cell model primary hepatocytes that the mechanical compaction on cell aggregates simulated by using transient centrifugation can directly activate the expression of HNF4α promoters. Moreover, data using primary hepatocytes showed that the HNF4α expression is positively associated with the levels of compaction force: 2.1-folds higher at the mRNA level and 2.1-folds higher at the protein level for 500 g vs. 0 g. Furthermore, activated HNF4α expression is associated with the enhanced biliary canalicular formation and the increased production of albumin and urea. Pretreatment with Latrunculin B, an inhibitor of F-actin, and SHE78-7, an inhibitor of E-cadherin, which both interrupt the pathway of mechanical transduction, partially but significantly reduced the HNF4α expression and production of albumin and urea. In conclusion, HNF4α can be actively involved in the hepatic polarization in the context of environmental mechanical compaction.
Acute, Subacute, and Genotoxicity Assessments of a Proprietary Blend of Garcinia mangostana Fruit Rind and Cinnamomum tamala Leaf Extracts (CinDura®)

The present communication describes a battery of toxicity studies that include an acute oral toxicity, a subacute twenty-eight-day repeated oral dose toxicity, and genotoxicity studies on a herbal formulation CinDura® (GMCT). This proprietary herbal composition contains the extracts of the Garcinia mangostana fruit rind (GM) and the Cinnamomum tamala leaf (CT). The toxicological evaluations were performed following the Organization for Economic Cooperation and Development (OECD) guidelines. The acute oral toxicity study in Wistar rats suggests that the median lethal dose of CinDura® is at least 2000 mg/kg body weight. Acute dermal and eye irritation tests in New Zealand white rabbits indicate that the test item is nonirritant to the skin and eyes. A twenty-eight-day repeated dose oral toxicity study was conducted in male and female Wistar rats using daily doses of 250, 500, and 1000 mg/kg body weight, followed by a fourteen-day reversal period for two satellite groups. The CinDura®-supplemented animals did not show any sign of toxicity on their body weights, organ weights, and on the hematobiochemical parameters. The gross pathology and histopathological examinations indicated no treatment-related changes in the experimental animals. Overall, the no-observed-adverse-effect level (NOAEL) of the herbal blend is 1000 mg/kg body weight, the highest tested dose. Also, the results of the bacterial reverse mutation test and the erythrocyte micronucleus assay in mouse bone marrow suggest that CinDura® (GMCT) is neither mutagenic nor clastogenic.
Differential Efficacy of Glycoside Hydrolases to Disperse Biofilms

Chronic wounds will impact 2% of the United States population at some point in their life. These wounds are often associated with a reoccurring, chronic infection caused by a community of microorganisms encased in an extracellular polymeric substance (EPS), or a biofilm. Biofilm-associated microbes can exhibit tolerance to antibiotics, which has prompted researchers to investigate therapeutics that improve antibiotic efficacy. Glycoside hydrolases (GHs), enzymes that target the polysaccharide linkages within the EPS, are one potential adjunctive therapy. In order to develop GH-based therapeutics, it is imperative that we understand whether the composition of biofilm EPS changes based on the environment and/or presence of other microbes. Here, we utilized α-amylase and cellulase to target the polysaccharides within the EPS of mono- and dual-species Pseudomonas aeruginosa and Staphylococcus aureus biofilms in three different models that vary in clinical relevancy. We show that biofilms established in an in vitro well-plate model are not strongly adhered to the polystyrene surface and do not accurately reflect the GH efficacy seen with biofilms grown in vivo. However, dispersal efficacy in an in vitro wound microcosm model was more reflective of that seen in a murine wound model. We also saw a striking loss of efficacy for cellulase to disperse S. aureus in both mono- and dual species biofilms grown in the wound models, suggesting that EPS constituents may be altered depending on the environment.
An Exploratory Clinical Study on an Automated, Speed-Sensing Treadmill Prototype With Partial Body Weight Support for Hemiparetic Gait Rehabilitation in Subacute and Chronic Stroke Patients

Impairments in walking speed, capacity, and endurance are commonly seen after stroke. Treadmill training improves endurance and gait speed. However, the lack of variable training speed and automated speed progression increases the risk of backward displacement and falling. An automated, speed-sensing treadmill prototype with partial body weight support, the Variable Automated Speed and Sensing Treadmill II (VASST II), was tested in an outpatient rehabilitation setting. Eleven subacute or chronic hemiplegics who could ambulate at > 0.2 m/s for >50 m participated in the study. All subjects underwent physiotherapist-supervised training on VASST II for 60 min daily, 3 times per week, for 5 weeks (total 15 h). Outcome measures at Week 3 (mid-VASST II training), Week 6 (post-VASST II training), Week 12 (first follow-up), and Week 24 (second follow-up) included the 6 minute walk test (6 MWT), 10 meter walk test (10 MWT), Berg Balance Scale (BBS) score, and Functional Ambulation category (FAC) score. User acceptability of VASST II for both study subjects and physiotherapists were also assessed. All subjects [median (IQR) age: 53.0 (22) years; median (IQR) duration post-stroke: 524 (811) days] completed VASST II training. At baseline, mean ± SD 6 MWT was 114 ± 50.9 m; mean ± SD 10 MWT was 0.37 ± 0.18 m/s; mean ± SD BBS score was 40 ± 10; and, mean ± SD FAC score was 4 ± 1. At Week 6, there were significant improvements in the 6 MWT [158.91 ± 88.69 m; P = 0.003], 10 MWT [0.49 ± 0.30 m/s; P = 0.016], and BBS score [42 ± 10; P = 0.003]. Improvements in 6 MWT and BBS scores were sustained at Week 24, but not in the 10 MWT. No VASST II-training related falls were reported. All subjects rated their VASST II training positively and indicated that it improved their current walking ability. VASST II training was effective, feasible, and safe in patients with subacute or chronic post-stroke hemiparetic gait, with sustained gains in distance walked (6 MWT) and functional balance (BBS score) up to 19 weeks post-intervention.