Miracle-dz/UniFAR-FTUs huggingface dataset:
A new method for characterizing surface roughness and available space in biological systems

1. Surface roughness and available space for organisms inhabiting heterogeneous habitats have important effects on measurements of species diversity, population abundance and dispersal. Quantifying habitat complexity is important but very difficult to achieve, especially at small scales. 2. A method of quantifying topographic roughness is described, which produces estimates of space potentially available to organisms in different size classes rather than giving general descriptors. The method uses samples of profiles across the surface of interest that are taken over any spatial scale and that are then analysed by a low-cost, image-processing technique. 3. A case study shows that the method allows quantification of the effects of surface texture on abundance of stream algae. Stream stones differing in geological rock type differed in roughness at very small spatial scales (crevices < 0.4 mm in size). Chlorophyll a concentrations were correlated positively with roughness measured at the smallest spatial scale (0.2 mm). A colonization experiment, in which bricks were sandblasted to produce rough surfaces, showed that rough substrata attain higher abundances of stream algae than smooth. The imaging technique permitted the quantification of the exact differences in texture between smooth and rough surfaces while demonstrating that both rough and smooth bricks still fell within the natural range of texture shown by stream stones
Portable Automatic Microring Resonator System Using a Subwavelength Grating Metamaterial Waveguide for High-Sensitivity Real-Time Optical-Biosensing Applications

The slow light sensor techniques have been applied to bio-related detection in the past decades. However, similar testing-systems are too large to carry to a remote area for diagnosis or point-of-care testing. This study demonstrated a fully automatic portable biosensing system based on the microring resonator. An optical-fiber array mounted on a controller based micro-positioning system, which can be interfaced with MATLAB to locate a tentative position for light source and waveguide coupling alignment. Chip adapter and microfluidic channel could be packaged as a product such that it is cheap to be manufactured and can be disposed of after every test conducted. Thus, the platform can be more easily operated via an ordinary user without expertise in photonics. It is designed based on conventional optical communication wavelength range. The C-band superluminescent-light-emitting-diode light source couples in/out the microring sensor to obtain quasi-TE mode by grating coupler techniques. For keeping a stable chemical binding reaction, the cost-effective microfluidic pump was developed to offer a specific flow rate of 20 μL/min by using a servo-motor, an Arduino board, and a motor driver. The subwavelength grating metamaterial ring resonator shows highly sensitive sensing performance via surface index changes due to biomarker adhered on the sensor. The real-time peak-shift monitoring shows 10 μg/mL streptavidin detection of limit based on the biotin-streptavidin binding reaction. Through the different specific receptors immobilized on the sensor surface, the system can be utilized on the open applications such as heavy metal detection, gas sensing, virus examination, and cancer marker diagnosis.
Endoscopic Ultrasound-Guided, Percutaneous, and Transjugular Liver Biopsy: A Comparative Systematic Review and Meta-Analysis

Background/Aims Percutaneous liver biopsy (PCLB) or transjugular liver biopsy (TJLB) have traditionally been performed to obtain a sample of hepatic tissue; however, endoscopic ultrasound-guided liver biopsy (EUSLB) has become an attractive alternative. The aim of this study was to compare the efficacy and safety of EUSLB, PCLB, and TJLB. Methods Search strategies were developed in accordance with PRISMA and MOOSE guidelines. Major outcomes included the following: adequacy of biopsy specimens (i.e., complete portal triads [CPT], total specimen length [TSL] in mm, and length of longest piece [LLP]) in mm), and rate of adverse events. Only studies comparing all biopsy approaches (i.e., EUSLB, PCLB, and TJLB) were included. Results Five studies (EUSLB [n=301]; PCLB [n=176]; and TJLB [n=179]) were included. Biopsy cumulative adequacy rates for EUSLB, PCLB, and TJLB were 93.51%, 98.27%, and 97.61%, respectively. Based on the subgroup analysis limited to EUS biopsy needles in current clinical practice, there was no difference in biopsy adequacy or adverse events for EUSLB compared to PCLB and TJLB (all p>0.050). A comparison of EUSLB and PCLB revealed no difference between specimens regarding both CPT (p=0.079) and LLP (p=0.085); however, a longer TSL (p<0.001) was observed. Compared to TJLB, EUSLB showed no difference in LLP (p=0.351), fewer CPT (p=0.042), and longer TSL (p=0.005). Conclusions EUSLB appears to be a safe, minimally invasive procedure that is comparable to PCLB and TJLB regarding biopsy specimens obtained and rate of adverse events associated with each method.
TRPpathies

Many human diseases are caused by mutations in ion channels. Dissecting the pathogenesis of these ‘channelopathies’ has yielded important insights into the regulation of vital biological processes by ions and has become a productive tool of modern ion channel biology. One of the best examples of a synergism between the clinical and basic science aspects of a modern biological topic is cystic fibrosis. Not only did the identification of the ion channel mutated in cystic fibrosis pinpoint the root cause of this disease, but it also has significantly advanced our understanding of basic biological processes as diverse as protein folding and epithelial fluid and electrolyte secretion. The list of confirmed ‘channelopathies’ is growing and several members of the TRP family of ion channels have been implicated in human diseases such as mucolipidosis type IV (MLIV), autosomal dominant polycystic kidney disease (ADPKD), familial focal segmental glomerulosclerosis (FSG), hypomagnesemia with secondary hypocalcaemia (HSH), and several forms of cancer. Analysing pathogenesis of the diseases linked to TRP dysregulation provides an exciting means of identifying novel functions of TRP channels.
Risk of injury after emergency department visit for acute peripheral vertigo: a matched-cohort study

Objective Peripheral vertigo is one of the most common causes of the emergency department (ED) visits. It can impair balance and might predispose patients to injuries after discharge. The purpose of this study was to determine whether peripheral vertigo is associated with an increased risk of trauma. Methods This matched-cohort study used the nationally representative dataset of de-identified claim information of 1 million randomly sampled individuals from a real Korean population, from 2002 to 2013. The exposure cohort included patients who visited EDs for new-onset peripheral vertigo without prior or concurrent injury. Each patient was randomly matched to five unexposed individuals (also without previous injury) by incidence density sampling. The primary outcome was a new injury within 1 year. The secondary outcomes were various injury subtypes. The time-dependent effect of the exposure was modeled using the extended Cox model. Age, sex, comorbidities, and household income level were included as covariates. Results A total of 776 and 3,880 individuals were included as the exposure and comparison cohorts, respectively. The risks of trunk injury and upper extremity injury were significantly higher in the exposure cohort. Extended Cox models with multivariable adjustment showed significantly increased risk for up to 1 year, with the first 1-month; 1 month to 3 months; and 3 months to 1 year hazard ratios of 5.23 (95% confidence interval [CI], 2.83–9.64); 1.50 (95% CI, 1.02–2.20); and 1.37 (95% CI, 1.11–1.68), respectively. Conclusion Patients visiting EDs for acute peripheral vertigo are at a higher risk of a new injury for up to a year.
Transcriptome Analysis of Psacothea hilaris: De Novo Assembly and Antimicrobial Peptide Prediction

Simple Summary Multidrug resistance for classical antibiotics is the major problem faced in clinical infections. Insects have antimicrobial peptides (AMPs) which are a part of the immune repertoire to protect it from microbial pathogens. AMPs are short chain protein molecules that function as antibacterial, antifungal, antiparasitic and antiviral factors. Insect AMPs are present in their hemolymph or produced in response to entry of pathogens and kill them to protect the host. The objective of this study is to identify novel AMPs from Psacothea hilaris, the yellow spotted long horned beetle. The beetle was immunized with bacteria and fungi and RNA was isolated. The RNA was processed and screened by in silico strategies to identify novel AMPs. We obtained one potential candidate which was tested to be effective against harmful bacteria and fungi. This will be useful in treating multidrug resistant microbes alone or in combination with antibiotics with future validations. Abstract Antimicrobial peptides (AMPs) are the frontline innate defense system evolutionarily preserved in insects to combat invading pathogens. These AMPs could serve as an alternative to classical antibiotics to overcome the burden of treating multidrug resistant bacteria. Psacotheasin, a knottin type AMP was isolated from Psacothea hilaris and shown to exhibit antimicrobial activity, especially against fungi through apoptosis mediated cell death. In this study, we aimed to identify novel probable AMPs from Psacothea hilaris, the yellow spotted longicorn beetle. The beetle was immunized with the two bacterial strains (E. coli and S. aureus), and the yeast strain C. albicans. After immunization, total RNA was isolated and sequenced in Illumina platform. Then, beetle transcriptome was de novo assembled and searched for putative AMPs with the known physiochemical features of the AMPs. A selection of AMP candidates were synthesized and tested for antimicrobial activity. Four peptides showed stronger activity against E. coli than the control AMP, melittin while one peptide showed similar activity against S. aureus. Moreover, four peptides and two peptides showed antifungal activity stronger than and similar to melittin, respectively. Collectively one peptide showed both antibacterial and antifungal activity superior to melittin; thus, it provides a potent antimicrobial peptide. All the peptides showed no hemolysis in all the tested concentrations. These results suggest that in silico mining of insects’ transcriptome could be a promising tool to obtain and optimize novel AMPs for human needs.
Whole‐exome sequencing identified two novel mutations of DYNC2LI1 in fetal skeletal ciliopathy

Skeletal ciliopathies are a group of clinically and genetically heterogeneous disorders with the spectrum of severity spanning from relatively mild to prenatally lethal. The aim of our study was to identify pathogenic mutations in a Chinese family with two siblings presenting a Short‐rib polydactyly syndrome (SRPS)‐like phenotype.
Smart Contract-Based Cross-Domain Authentication and Key Agreement System for Heterogeneous Wireless Networks

Nowadays, it is still a major challenge to design a secure cross-domain authentication protocol for heterogeneous wireless networks with different security parameters. As a new technology, blockchain has attracted people’s attention because of its tamper-proof and decentralized characteristics. In this paper, we propose a cross-domain authentication and key agreement system based on smart contract of blockchains. Public keys of the nodes are managed using the smart contracts, and the system parameters are confirmed by contract query. On this basis, a cross-domain authentication and key agreement protocol is designed. In this protocol, roaming users can select temporary authentication parameters according to the system parameters of the roaming domain to complete authentication and key agreement, and users are anonymous in the process. Security of the protocol is demonstrated under the CK model, and two formal analysis tools are used to further analyze the protocol. Since the protocol does not have complex cryptographic operations and certificate verification, it has lower computational and communication overhead.
Attention‐deficit/hyperactivity disorder symptoms and dietary habits in adulthood: A large population‐based twin study in Sweden

Associations between adult attention‐deficit/hyperactivity disorder (ADHD) symptoms and dietary habits have not been well established and the underlying mechanisms remain unclear. We explored these associations using a Swedish population‐based twin study with 17,999 individuals aged 20–47 years. We estimated correlations between inattention and hyperactivity/impulsivity with dietary habits and fitted twin models to determine the genetic and environmental contributions. Dietary habits were defined as (a) consumption of food groups, (b) consumption of food items rich in particular macronutrients, and (c) healthy and unhealthy dietary patterns. At the phenotypic level, inattention was positively correlated with seafood, high‐fat, high‐sugar, high‐protein food consumptions, and unhealthy dietary pattern, with correlation coefficients ranging from 0.03 (95%CI: 0.01, 0.05) to 0.13 (95% CI: 0.11, 0.15). Inattention was negatively correlated with fruits, vegetables consumptions and healthy dietary pattern, with correlation coefficients ranging from −0.06 (95%CI: −0.08, −0.04) to −0.07 (95%CI: −0.09, −0.05). Hyperactivity/impulsivity and dietary habits showed similar but weaker patterns compared to inattention. All associations remained stable across age, sex and socioeconomic status. Nonshared environmental effects contributed substantially to the correlations of inattention (56–60%) and hyperactivity/impulsivity (63–80%) with dietary habits. The highest and lowest genetic correlations were between inattention and high‐sugar food (rA = .16, 95% CI: 0.07, 0.25), and between hyperactivity/impulsivity and unhealthy dietary pattern (rA = .05, 95% CI: −0.05, 0.14), respectively. We found phenotypic and etiological overlap between ADHD and dietary habits, although these associations were weak. Our findings contribute to a better understanding of common etiological pathways between ADHD symptoms and various dietary habits.
Superficial white matter imaging: Contrast mechanisms and whole-brain in vivo mapping

Superficial white matter mapping provides the foundation for systematic studies of this crucial structure. Superficial white matter (SWM) contains the most cortico-cortical white matter connections in the human brain encompassing the short U-shaped association fibers. Despite its importance for brain connectivity, very little is known about SWM in humans, mainly due to the lack of noninvasive imaging methods. Here, we lay the groundwork for systematic in vivo SWM mapping using ultrahigh resolution 7 T magnetic resonance imaging. Using biophysical modeling informed by quantitative ion beam microscopy on postmortem brain tissue, we demonstrate that MR contrast in SWM is driven by iron and can be linked to the microscopic iron distribution. Higher SWM iron concentrations were observed in U-fiber–rich frontal, temporal, and parietal areas, potentially reflecting high fiber density or late myelination in these areas. Our SWM mapping approach provides the foundation for systematic studies of interindividual differences, plasticity, and pathologies of this crucial structure for cortico-cortical connectivity in humans.
GC-MS analysis of volatiles in cinnamon essential oil extracted by different methods ; Análisis de volátiles mediante GC-MS de aceites esenciales de canela extraídos por diferentes métodos

Cinnamon essential oil (CEO) was extracted by three different methods: steam distillation (SD), ultrasound-assisted steam distillation (UASD) and microwave-assisted steam distillation (MASD). The volatiles in CEO were separated and identified by gas chromatography–mass spectrometry (GC-MS), and the differences in volatiles among the three different methods were further analyzed through principal component analysis. The results showed that 36 individual volatile components were present in the CEO from the three different methods. In general, the numbers of aldehydes, esters, alcohols, terpenes, aromatics and ketones were 6, 3, 7, 17, 2, and 1, respectively. The most abundant volatile component was determined to be cinnamic aldehyde. The content of total cinnamic aldehydes, which determines the price of CEO, was the highest among the three methods in the UASD sample (85.633%). Moreover, the highest yield (8.33‰) of essential oil was extracted by the UASD method. Therefore, UASD was the best way for CEO extraction in this research and was recommended for future industrial applications.
Transcriptomic analysis reveals a WNT signaling pathway-based gene signature prognostic for non-small cell carcinoma

The value of combining multiple candidate genes into a panel to improve biomarker performance is increasingly emphasized. Genes associated with WNT signaling are widely-reported to provide prognostic signatures in non-small cell carcinoma (NSCLC). Screening of genes involved in this signaling pathway facilitated selection of an optimal candidate biomarker gene combination and development of an NSCLC prognostic model based on expression of these genes. Risk scores derived from the model performed well in predicting survival; in the training dataset, samples achieving a high risk score exhibit a shorter survival interval (median survival time 34.8 months, 95% CI 31.1-41.0) than did samples achieving a low risk score (median survival time 72.0 months, 95% CI 59.3-87.5, p=2e-11), and exhibited higher oncogene and lower tumor suppressor gene expression. Receiver-operator characteristic curves based on three-year survival demonstrate that the model outperformed clinical prognostic indicators. In addition, the model was validated in four independent cohorts, demonstrating robust NSCLC prognostic value. Correlation analyses reveal that the model offers efficacy independent of other clinical indicators. Gene Set Enrichment Analysis (GSEA) reveals that the model reflects variable tissue functional states relevant to NSCLC biology. In summary, the signature model shows potential as a valuable and robust NSCLC prognostic indicator.
EGG SIZE IN ARCTIC, ANTARCTIC AND DEEP‐SEA FISHES

deep-sea species. His summarized data for the first four families are listed in table 1. Antarctic fishes from the coastal zones: In only one species (or two, if Bouvet Island is included in the Antarctic region) are the sizes of the free eggs known. The measurements of all others have been made from an examination of the ovaries. 1. 'hese are indicated (table 2) by the plus sign following the dimensions. indicating that the eggs are at least of this size. since there is likely to be an increase in the diameter of the eggs after fertilization and laying. Measurements (or data) on ripe or ripening ovarian eggs only have been taken, this being particularly indicated by the orange-yellow or brownish-yellow color of such eggs. Immature eggs always appear to be whitish, which can be clearly seen in ovaries containing more than one generation of eggs. The measurements are all in millimeters. Finally it may be conveniently noted here that judging from the distribution of the early larval stages, which have been taken almost entirely in coastal waters, and the finding of the eggs of H arpagifer bispinis in shallow water at Port Lockroy, Palmer Archipelago and those of a nototheniid near Bouvet Island (in 119 to 124 meters), the coastal fishes as far as known lay their eggs in relatively shallow waters. Since the tendency of arctic fishes to produce relatively large, yolky eggs has been considered by Rass (1941), it will only be necessary to discuss the data for antarctic species. Comparing representatives of the genus Notothenia from the Falkland Islands with species of other nototheniiform genera liv-
Blood extracellular vesicles from healthy individuals regulate hematopoietic stem cells as humans age

Hematopoietic stem cells (HSCs) maintain balanced blood cell production in a process called hematopoiesis. As humans age, their HSCs acquire mutations that allow some HSCs to disproportionately contribute to normal blood production. This process, known as age‐related clonal hematopoiesis, predisposes certain individuals to cancer, cardiovascular and pulmonary pathologies. There is a growing body of evidence suggesting that factors outside cells, such as extracellular vesicles (EVs), contribute to the disruption of stem cell homeostasis during aging. We have characterized blood EVs from humans and determined that they are remarkably consistent with respect to size, concentration, and total protein content, across healthy subjects aged 20–85 years. When analyzing EV protein composition from mass spectroscopy data, our machine‐learning‐based algorithms are able to distinguish EV proteins based on age and suggest that different cell types dominantly produce EVs released into the blood, which change over time. Importantly, our data show blood EVs from middle and older age groups (>40 years) significantly stimulate HSCs in contrast to untreated and EVs sourced from young subjects. Our study establishes for the first time that although EV particle size, concentration, and total protein content remain relatively consistent over an adult lifespan in humans, EV content evolves during aging and potentially influences HSC regulation.
Breast cancer genetics and managed care

In 1996, with evolution of the science of cancer genetics and the advent of commercially available BRCA1 and later BRCA2 testing, Kaiser Permanente began to apply these advances in clinical practice. Recommendations for referral to genetic counseling were developed in 1997 as the Clinical Practice Guidelines for Referral for Genetic Counseling for Inherited Susceptibility for Breast and Ovarian Cancer. Implementation of these guidelines with associated protocols in Kaiser Permanente's Northern California Region has occupied the ensuing years and includes dissemination of the high‐risk guidelines for breast and ovarian cancer, dissemination of patient and physician educational materials on the breast cancer guidelines, monthly classes and taped healthphone messages for patients, interactive videoconferencing for physicians, a training seminar for medical geneticists who will counsel patients at risk, publication of articles on breast cancer and genetic risk in health plan member–and physician‐directed magazines, identification and training of clinical specialists and supporting clinicians to care for patients before and after counseling, individual counseling and testing of patients and families, and development of a data registry. Implementing the guidelines helped us communicate the uncertainty surrounding breast cancer testing, and we were obliged to learn more about ethical, legal, societal, and insurance controversies surrounding genetic testing. Given the lack of effective prevention for breast or ovarian cancer and the difficulty of treatment, the appropriate use of genetics in patient care is essential. In the near future, we will see the need for cancer genetics to become an integral part of practice throughout the spectrum of health care. We at Kaiser Permanente feel that the breast cancer guideline project is the first step in this process. Cancer 1999;86:1750–4. © 1999 American Cancer Society.