Miracle-dz/UniFAR-FTUs huggingface dataset:
An ecologically motivated image dataset for deep learning yields better models of human vision

Significance Inspired by core principles of information processing in the brain, deep neural networks (DNNs) have demonstrated remarkable success in computer vision applications. At the same time, networks trained on the task of object classification exhibit similarities to representations found in the primate visual system. This result is surprising because the datasets commonly used for training are designed to be engineering challenges. Here, we use linguistic corpus statistics and human concreteness ratings as guiding principles to design a resource that more closely mirrors categories that are relevant to humans. The result is ecoset, a collection of 1.5 million images from 565 basic-level categories. We show that ecoset-trained DNNs yield better models of human higher-level visual cortex and human behavior. Deep neural networks provide the current best models of visual information processing in the primate brain. Drawing on work from computer vision, the most commonly used networks are pretrained on data from the ImageNet Large Scale Visual Recognition Challenge. This dataset comprises images from 1,000 categories, selected to provide a challenging testbed for automated visual object recognition systems. Moving beyond this common practice, we here introduce ecoset, a collection of >1.5 million images from 565 basic-level categories selected to better capture the distribution of objects relevant to humans. Ecoset categories were chosen to be both frequent in linguistic usage and concrete, thereby mirroring important physical objects in the world. We test the effects of training on this ecologically more valid dataset using multiple instances of two neural network architectures: AlexNet and vNet, a novel architecture designed to mimic the progressive increase in receptive field sizes along the human ventral stream. We show that training on ecoset leads to significant improvements in predicting representations in human higher-level visual cortex and perceptual judgments, surpassing the previous state of the art. Significant and highly consistent benefits are demonstrated for both architectures on two separate functional magnetic resonance imaging (fMRI) datasets and behavioral data, jointly covering responses to 1,292 visual stimuli from a wide variety of object categories. These results suggest that computational visual neuroscience may take better advantage of the deep learning framework by using image sets that reflect the human perceptual and cognitive experience. Ecoset and trained network models are openly available to the research community.
Dual-crosslinked 3D printed gelatin scaffolds with potential for temporomandibular joint cartilage regeneration

A promising alternative to current treatment options for degenerative conditions of the temporomandibular joint (TMJ) is cartilage tissue engineering, using 3D printed scaffolds and mesenchymal stem cells. Gelatin, with its inherent biocompatibility and printability has been proposed as a scaffold biomaterial, but because of its thermoreversible properties, rapid degradation and inadequate strength it must be crosslinked to be stable in physiological conditions. The aim of this study was to identify non-toxic and effective crosslinking methods intended to improve the physical properties of 3D printed gelatin scaffolds for cartilage regeneration. Dehydrothermal (DHT), ribose glycation and dual crosslinking with both DHT and ribose treatments were tested. The crosslinked scaffolds were characterized by chemical, mechanical, and physical analysis. The dual-crosslinked scaffolds had the highest degree of crosslinking and the greatest resistance to hydrolytic and enzymatic degradation. Compared to the dual-crosslinked group, the ribose-crosslinked scaffolds had thinner printed strands, larger pore surface area and higher fluid uptake. The compressive modulus values were 2 kPa for ribose, 37.6 kPa for DHT and 30.9 kPa for dual-crosslinked scaffolds. None of the crosslinking methods had cytotoxic effects on the seeded rat bone marrow-derived mesenchymal stem cells (rBMSC). After 4 and 7 d, the dual-crosslinked scaffolds exhibited better cell proliferation than the other groups. Although all scaffolds supported chondrogenic differentiation of rBMSC, dual-crosslinked scaffolds demonstrated the lowest expression of the hypertrophy-related collagen 10 gene after 21 d. The results show that 3D printed gelatin scaffolds, when dually crosslinked with ribose and DHT methods, are not toxic, promote chondrogenic differentiation of rBMSC and have potential application in tissue engineering of TMJ condylar cartilage.
Revised Formulation for the Refractive Index of Water and Steam as a Function of Wavelength, Temperature and Density

Schiebener et al. published a formulation for the refractive index of water and steam in 1990 [J. Phys. Chem. Ref. Data 19, 677 (1990)]. It covered the ranges 0.2 to 2.5 μm in wavelength, −12 to 500 °C in temperature, and 0 to 1045 kg m−3 in density. The formulation was adopted by the International Association for the Properties of Water and Steam (IAPWS) in 1991. In the present article, the data, after conversion to ITS-90, have been refitted to the same functional form, but based on an improved equation of state for water adopted by IAPWS in 1995. The revised coefficients are reported, and some tabular material is provided. The revised refractive-index formulation was adopted by IAPWS in 1997 and is available as part of a National Institute of Standards and Technology Standard Reference Database. For most conditions, the revised formulation does not differ significantly from the previous one. A substantial improvement has been obtained in supercooled water at ambient pressure, where the previous formula.
Multinodal Acoustic Trapping Enables High Capacity and High Throughput Enrichment of Extracellular Vesicles and Microparticles in miRNA and MS Proteomics Studies

We report a new design of an acoustophoretic trapping device with significantly increased capacity and throughput, compared to current commercial acoustic trapping systems. Acoustic trapping enables nanoparticle and extracellular vesicle (EV) enrichment without ultracentrifugation. Current commercial acoustic trapping technology uses an acoustic single-node resonance and typically operates at flow rates <50 μL/min, which limits the processing of the larger samples. Here, we use a larger capillary that supports an acoustic multinode resonance, which increased the seed particle capacity 40 times and throughput 25–40 times compared to single-node systems. The resulting increase in capacity and throughput was demonstrated by isolation of nanogram amounts of microRNA from acoustically trapped urinary EVs within 10 min. Additionally, the improved trapping performance enabled isolation of extracellular vesicles for downstream mass spectrometry analysis. This was demonstrated by the differential protein abundance profiling of urine samples (1–3 mL), derived from the non-trapped versus trapped urine samples.
Optical coherence tomography of arteriolar diameter and capillary perfusion during spreading depolarizations

Spreading depolarization (SD) is associated with profound oligemia and reduced oxygen availability in the mouse cortex during the depolarization phase. Coincident pial arteriolar constriction has been implicated as the primary mechanism for the oligemia. However, where in the vascular bed the hemodynamic response starts has been unclear. To resolve the origin of the hemodynamic response, we used optical coherence tomography (OCT) to simultaneously monitor changes in the vascular tree from capillary bed to pial arteries in mice during two consecutive SDs 15 minutes apart. We found that capillary flow dropped several seconds before pial arteriolar constriction. Moreover, penetrating arterioles constricted before pial arteries suggesting upstream propagation of constriction. Smaller caliber distal pial arteries constricted stronger than larger caliber proximal arterioles, suggesting that the farther the constriction propagates, the weaker it gets. Altogether, our data indicate that the hemodynamic response to cortical SD originates in the capillary bed.
The presence and progression of choroidal neurofibromas in a predominantly pediatric population with neurofibromatosis type-1

ABSTRACT Background: Obtaining a definitive neurofibromatosis type-1 (NF1) diagnosis may take years. The natural history of choroidal neurofibromas in NF1 is unknown. This study evaluates a predominantly pediatric patient cohort for ocular features in NF1, including presence and progression of choroidal abnormalities, to determine their natural history, relationship to other NF1 features, and additive value in NF1 diagnosis. Methods: Retrospective analysis of 106 patients referred for Ophthalmic monitoring or diagnosis of NF1 between January 2012 and December 2018. Clinical records and Near-Infrared Reflectance (NIR) Optical Coherence Tomography imaging were analyzed for prevalence and progression of choroidal neurofibromas on NIR, and relation to other NF1 diagnostic criteria. Results: 54.7% of patients referred had a confirmed NF1 diagnosis, and 45.4% were NF1 suspects. First ophthalmic review resulted in an additional 6.6% patients meeting the diagnostic criteria, and 14.2% later developed sufficient features (total n = 80). Choroidal neurofibromas were present in 75.7% of patients that had NIR imaging and met diagnostic criteria, and detected in the absence of, or prior to Lisch nodules in 13.5%. Progression in the size and number of choroidal neurofibromas occurred in 26 eyes (32.5%) of 14 patients (35.0%), all under 16 years old. Patients without choroidal neurofibromas at first examination never developed them over the study period. Conclusion: Choroidal neurofibromas, detected by NIR imaging, are common in NF1, present early with frequent progression, and represent an additional tool to aid NF1 diagnosis in young children.
Lack of association between heart period variability asymmetry and respiratory sinus arrhythmia in healthy and chronic heart failure individuals

Temporal asymmetry is a peculiar aspect of heart period (HP) variability (HPV). HPV asymmetry (HPVA) is reduced with aging and pathology, but its origin is not fully elucidated. Given the impact of respiration on HPV resulting in the respiratory sinus arrhythmia (RSA) and the asymmetric shape of the respiratory pattern, a possible link between HPVA and RSA might be expected. In this study we tested the hypothesis that HPVA is significantly associated with RSA and asymmetry of the respiratory rhythm. We studied 42 middle-aged healthy (H) subjects, and 56 chronic heart failure (CHF) patients of whom 26 assigned to the New York Heart Association (NYHA) class II (CHF-II) and 30 to NYHA class III (CHF-III). Electrocardiogram and lung volume were monitored for 8 minutes during spontaneous breathing (SB) and controlled breathing (CB) at 15 breaths/minute. The ratio of inspiratory (INSP) to expiratory (EXP) phases, namely the I/E ratio, and RSA were calculated. HPVA was estimated as the percentage of negative HP variations, traditionally measured via the Porta’s index (PI). Departures of PI from 50% indicated HPVA and its significance was tested via surrogate data. We found that RSA increased during CB and I/E ratio was smaller than 1 in all groups and experimental conditions. In H subjects the PI was about 50% during SB and it increased significantly during CB. In both CHF-II and CHF-III groups the PI was about 50% during SB and remained unmodified during CB. The PI was uncorrelated with RSA and I/E ratio regardless of the experimental condition and group. Pooling together data of different experimental conditions did not affect conclusions. Therefore, we conclude that the HPVA cannot be explained by RSA and/or I/E ratio, thus representing a peculiar feature of the cardiac control that can be aroused in middle-aged H individuals via CB.
Adult lifetime cost of hemophilia B management in the US: payer and societal perspectives from a decision analytic model

Abstract Aims Hemophilia B (HB) is a rare congenital disorder characterized by bleeding-related complications which are managed by prophylactic or post-bleeding event (“on-demand”) replacement of clotting factor IX (FIX). The standard of care for severe HB is life-long prophylaxis with standard half-life (SHL) or extended half-life (EHL) products given every 2–3 or 7–14 days, respectively. FIX treatment costs in the US have been investigated, but the lifetime costs of HB treatment have not been well characterized, particularly related to the impact of joint health deterioration and associated health resource utilization. We developed a decision-analytic model to explore outcomes, costs and underlying cost drivers associated with FIX treatment options over the lifetime of an adult with severe or moderately severe HB. Materials and methods With participation from clinicians, health technology assessment specialists and patient advocates, a Markov model was constructed to estimate bleeding events and costs associated with health states including “bleed into joint”, “bleed not into joint”, “no bleed” and “death”. Sub-models of joint health were based on 0, 1, or ≥2 areas of chronic joint damage. US third-party payer and societal perspectives were considered with a lifetime horizon; sensitivity analyses tested the robustness of primary findings. Results Total adult lifetime costs per patient with severe and moderately severe HB were $21,086,607 for SHL FIX prophylaxis, $22,987,483 for EHL FIX prophylaxis, and $20,971,826 for on-demand FIX treatment. For FIX prophylaxis, the cost of FIX treatment accounts for >90% of the total HB treatment costs. Conclusions This decision analytic model demonstrated significant economic burden associated with the current HB treatment paradigm.
The KbvR Regulator Contributes to Capsule Production, Outer Membrane Protein Biosynthesis, Antiphagocytosis, and Virulence in Klebsiella pneumoniae

Klebsiella pneumoniae is an opportunistic pathogen that mostly affects patients with weakened immune systems, but a few serotypes (especially K1 and K2) are highly invasive and result in systemic infection in healthy persons. The ability to evade and survive the components of the innate immune system is critical in infection. To investigate the role and mechanism of transcription regulator KP1_RS12260 (KbvR) in virulence and defense against the innate immune response, kbvR deletion mutant and complement strains were constructed. The in vivo animal infection assay and in vitro antiphagocytosis assay demonstrate K. pneumoniae KbvR is an important regulator that contributes to virulence and the defense against phagocytosis of macrophages. ABSTRACT Klebsiella pneumoniae is an opportunistic pathogen that mostly affects patients with weakened immune systems, but a few serotypes (especially K1 and K2) are highly invasive and result in systemic infection in healthy persons. The ability to evade and survive the components of the innate immune system is critical in infection. To investigate the role and mechanism of transcription regulator KP1_RS12260 (KbvR) in virulence and defense against the innate immune response, kbvR deletion mutant and complement strains were constructed. The in vivo animal infection assay and in vitro antiphagocytosis assay demonstrate K. pneumoniae KbvR is an important regulator that contributes to virulence and the defense against phagocytosis of macrophages. The transcriptome analysis and phenotype experiments demonstrated that deletion of kbvR decreased production of capsular polysaccharide (CPS) and biosynthesis of partly outer membrane proteins (OMPs). The findings suggest that KbvR is a global regulator that confers pathoadaptive phenotypes, which provide several implications for improving our understanding of the pathogenesis of K. pneumoniae.
GC/MS Profiling, In Vitro and In Silico Pharmacological Screening and Principal Component Analysis of Essential Oils from Three Exotic and Two Endemic Plants from Mauritius

The chemical and pharmacological profiles of essential oils (EOs) hydrodistilled in yields of 0.03–0.77 % (w/w) from three exotic (Cinnamomum camphora, Petroselinum crispum, and Syzygium samarangense) and two endemic (Pittosporum senacia subsp. senacia and Syzygium coriaceum) medicinal plants were studied. GC‐MS/GC‐FID analysis of the EOs identified the most dominant components to be myristicin (40.3 %), myrcene (62.2 %), 1,8‐cineole (54.0 %), β‐pinene (21.3 %) and (E)‐β‐ocimene (24.4 %) in P. crispum, P. senacia and C. camphora, S. samarangense and S. coriaceum EOs, respectively. All EOs were found to possess anti‐amylase (0.70–1.50 mM ACAE/g EO) and anti‐tyrosinase (109.35–158.23 mg KAE/g) properties, whereas no glucosidase inhibition was displayed. Only Syzygium EOs acted as dual inhibitors of both acetyl‐ and butyryl‐cholinesterases, while P. senacia and C. camphora EOs inhibited acetylcholinesterase selectively and P. crispum EO was inactive (AChE: 4.64–4.96 mg GALAE/g; BChE: 5.96 and 7.10 mg GALAE/g). Molecular docking revealed 1,8‐cineole to present the best binding affinities with butyrylcholinesterase, amylase and tyrosinase, while both myristicin and β‐pinene with acetylcholinesterase and finally β‐pinene with glucosidase. In vitro antioxidant potency was also demonstrated in different assays (DPPH: 13.52–53.91 mg TE/g, ABTS: 5.49–75.62 mg TE/g; CUPRAC: 45.38–243.21 mg TE/g, FRAP: 42.49–110.64 mg TE/g; and phosphomolybdenum assay: 82.61–160.93 mM TE/g). Principal component analysis revealed the EOs to differ greatly in their bioactivities due to their chemodiversity. This study has unveiled some interesting preliminary pharmacological profiles of the EOs that could be explored for their potential applications as phytotherapeutics.
Taurine-Mediated IDOL Contributes to Resolution of Streptococcus uberis Infection

Metabolic alterations occur in pathogenic infections, but the role of lipid metabolism in the progression of bacterial mastitis is unclear. Cross talk between lipid droplets (LDs) and invading bacteria occurs, and targeting of de novo lipogenesis inhibits pathogen reproduction. ABSTRACT Metabolic alterations occur in pathogenic infections, but the role of lipid metabolism in the progression of bacterial mastitis is unclear. Cross talk between lipid droplets (LDs) and invading bacteria occurs, and targeting of de novo lipogenesis inhibits pathogen reproduction. In this study, we investigate the role(s) of lipid metabolism in mammary cells during Streptococcus uberis infection. Our results indicate that S. uberis induces the synthesis of fatty acids and production of LDs. Importantly, taurine reduces fatty acid synthesis, the abundance of LDs and the in vitro bacterial load of S. uberis. These changes are mediated, at least partly, by the E3 ubiquitin ligase IDOL, which is associated with the degradation of low-density lipoprotein receptors (LDLRs). We have identified a critical role for IDOL-mediated fatty acid synthesis in bacterial infection, and we suggest that taurine may be an effective prophylactic or therapeutic strategy for preventing S. uberis mastitis.
Counterfactual thinking in psychiatric and neurological diseases: A scoping review

Background The ability to simulate alternatives to factual events is called counterfactual thinking (CFT) and it is involved both in emotional and behavioral regulation. CFT deficits have been reported in psychiatric and neurological conditions, possibly contributing to patients’ difficulties in modulating behaviors and affections. Thus, acknowledging the presence and possible consequences of CFT impairments might be essential for optimal clinical management. Objectives This scoping review aims to summarize the previous evidence about CFT in psychiatric and neurological diseases to determine the extent of the previous research and what has been discovered so far, the variety of clinical conditions considered, the methodologies adopted, and the relevant issues to be addressed by future investigations. Methods PsycInfo, PubMed, Scopus, and Web of Science were searched to identify articles published up to January 2020, written in English and focused on CFT in adults affected by psychiatric or neurological conditions. Results Twenty-nine studies have been included; most of them focused on psychiatric conditions, a minority considered neurological diseases. The generation of counterfactual thoughts related to a negative real-life or a fictional event and the counterfactual inference test were the most popular tasks adopted. CFT impairments were reported in both psychiatric and neurological conditions, likely associated with a fronto-executive dysfunction. Conclusions Future research might further explore CFT in those psychiatric and neurological conditions in which CFT difficulties have been preliminary reported. Furthermore, it would be recommendable to extend this investigation to all the clinical conditions possibly at risk of fronto-executive dysfunction. In the end, we speculate that since CFT plays a role in driving everyday behaviors, it might be crucial also when medical decisions are involved; thus, future research might extend the investigation of CFT especially to those populations that implicate complex clinical management.
Determinants of peripheral neuropathy among diabetic patients under follow-up in chronic care clinics of public hospitals at Gamo and Gofa zones, southern Ethiopia

Background Peripheral neuropathy is a leading cause of morbidity and increased mortality among diabetic patients. It is characterized by significant deficits in vibration and tactile sensation. With an annual incidence of 2%, it affects as many as 110 million people worldwide. The aim of this study was to assess factors associated with peripheral neuropathy among diabetic patients in chronic care clinic in Gamo and Gofa zone, South Ethiopia. Methods An institution- based unmatched case control study was employed among 528 randomly selected participants using a pre-tested, interviewer-administered, and structured questionnaire. Bivariate and multivariable logistic regression analysis was conducted to identifiy determinants of peripheral neuropathy using IBM SPSS version 25. Result The odds of being an urban dweller was 2.67 times higher among cases than controls [AOR = 2.67 (1.27, 5.63)]. The likelihood of fasting blood glucose level between 203 and 282 and 282 and above was 2.55 and 3.88 times higher among cases than controls [AOR = 2.55 (1.91, 7.16)] and [AOR = 3.88 (1.42, 10.60)] respectively. The probability of living with diabetes mellitus for 10 and more years was 3.88 times higher among cases than controls [AOR = 3.88 (1.42, 10.60)]. The odds of controlling glucose level after developing symptom was 5.33 times higher among cases than controls [AOR = 5.33 (1.28, 12.24)]. The probability of having high blood pressure was 2.36 times higher among cases than controls [AOR = 2.36 (1.26, 4.43)]. The likelihood of having a family history of complication from diabetes mellitus was 5.60 times higher among cases than controls [AOR = 5.60 (2.03, 15.43)]. The odds of exercising 3 times per week for 15 to 30 minutes and for less than 15 minutes were 2.96 and 4.92 times higher among cases than controls respectively [AOR = 2.96 (1.32, 6.61)] and AOR = 4.92, 95% CI (1.85, 13.04) respectively. The likelihood of having a waist circumference greater than or equal to 40 inch was 2.72 times higher among cases than controls [AOR = 2.72 (1.07, 6.94)]. Conclusion This study showed that residence, duration of diabetic mellitus, family history of complication from diabetic mellitus, level of fasting blood glucose, method of glycemic control, having a high blood pressure/hypertension/, frequency and duration of physical activity and waist circumference were found to be determinants of peripheral neuropathy. Thus, the concerned health authorities and health professionals should target on these factors in their efforts to prevent peripheral neuropathy among diabetics in the study area.