Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of a gas-injection system during the FIB-TOF-SIMS analysis - influence of water and fluorine gases on secondary ion signals and sputtering rates.

Combining a Gas-Injection System (GIS) with the Focused Ion Beam (FIB) has a broad scope of applications in sample preparation such as protective layer deposition, increasing material sputtering rates and reducing FIB-related artefacts. On the other hand injecting certain specific gases during a Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) analysis can significantly increase element ionization probability and, therefore, improve the quality of 3D representation of a sample elemental structure. In this work, for the first time the potential of GIS for enhancing secondary ion signals acquired using a TOF detector incorporated into a commercial Ga+ FIB-SEM (Focused Ion Beam combined with Scanning Electron Microscope) instrument is presented. The depth profiles of pure metals (100 nm thick thin films of Cu, Zr, Ag and W) were acquired at ambient vacuum conditions as well as under an exposure to water and fluorine gases. The influence of supplementary gases on the ion yields and sputtering rates were studied. Simulations were performed to assess the local gas pressure at the location of FIB-TOF-SIMS analysis. The highest enhancement of ionization probability was achieved in the case of the Cu thin film (10 times during water co-injection and 510 times when using a fluorine gas). Regarding the sputtering rates, the response of Zr to effect of the gases was the strongest. Comparing to a standard background pressure measurements, this thin film was milled around 6 times faster under the exposure to a water vapor and over 2 times faster when fluorine gas was supplied.
Absolute Quantitation of Drug-Metabolizing Cytochrome P450 Enzymes and Accessory Proteins in Dog Liver Microsomes Using Label-Free Standard-Free Analysis Reveals Interbreed Variability

Dogs are commonly used in human and veterinary pharmaceutical development. Physiologically based pharmacokinetic modeling using recombinant cytochrome P450 (CYP) enzymes requires accurate estimates of CYP abundance, particularly in liver. However, such estimates are currently available for only seven CYPs, which were determined in a limited number of livers from one dog breed (beagle). In this study, we used a label-free shotgun proteomics method to quantitate 11 CYPs (including four CYPs not previously measured), cytochrome P450 oxidoreductase, and cytochrome b5 in liver microsomes from 59 dogs representing four different breeds and mixed-breed dogs. Validation included showing correlation with CYP marker activities, immunoquantified protein, as well as CYP1A2 and CYP2C41 null allele genotypes. Abundance values largely agreed with those previously published. Average CYP abundance was highest (>120 pmol/mg protein) for CYP2D15 and CYP3A12; intermediate (40–89 pmol/mg) for CYP1A2, CYP2B11, CYP2E1, and CYP2C21; and lowest (<12 pmol/mg) for CYP2A13, CYP2A25, CYP2C41, CYP3A26, and CYP1A1. The CYP2C41 gene was detected in 12 of 58 (21%) livers. CYP2C41 protein abundance averaged 8.2 pmol/mg in those livers, and was highest (19 pmol/mg) in the only liver with two CYP2C41 gene copies. CYP1A2 protein was not detected in the only liver homozygous for the CYP1A2 stop codon mutation. Large breed–associated differences were observed for CYP2B11 (P < 0.0001; ANOVA) but not for other CYPs. Research hounds and Beagles had the highest CYP2B11 abundance; mixed-breed dogs and Chihuahua were intermediate; whereas greyhounds had the lowest abundance. These results provide the most comprehensive estimates to date of CYP abundance and variability in canine liver. SIGNIFICANCE STATEMENT This work provides the most comprehensive quantitative analysis to date of the drug-metabolizing cytochrome P450 proteome in dogs that will serve as a valuable reference for physiologically based scaling and modeling used in drug development and research. This study also revealed high interindividual variation and dog breed–associated differences in drug–metabolizing cytochrome P450 expression that may be important for predicting drug disposition variability among a genetically diverse canine population.
Evaluation of recent evidence on the solubility of beryllium compounds and cancer risk

Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, Exponent Inc., Menlo Park, California and Exponent Inc., Bellevue, Washington, USA Correspondence to Paolo Boffetta, MD, MPH, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1130, New York, NY 10029, USA Tel: +1 212 824 7378; fax +1 212 849 2566; e-mail: paolo.boffetta@gmail.com
Evolution of pedal digit orientation and morphology in relation to acquisition and secondary loss of the adhesive system in geckos

Among geckos, the acquisition of the adhesive system is associated with several morphological changes of the feet that are involved in the operation of the adhesive apparatus. However, analyses using a comparative framework are lacking. We applied traditional morphometrics and geometric morphometric analysis with phylogenetic comparative methods to morphological data, collected from X‐ray scans, to examine patterns of morphological evolution of the pes in association with the gain and loss of adhesive capabilities, and with habitat occupancy among 102 species of gecko. Padbearing gecko lineages tend to have shorter digits and greater inter‐digital angles than padless ones. Arboreal and saxicolous species have shorter digits than terrestrial species. Our results suggest repeated shifts that converge upon a similar padbearing morphology, with some modifications being associated with the habitat occupied. We demonstrate that functional innovation and habitat can operate on, and influence, different components of foot morphology.
Composition, physicochemical properties of pea protein and its application in functional foods

Abstract Field pea is one of the most important leguminous crops over the world. Pea protein is a relatively new type of plant proteins and has been used as a functional ingredient in global food industry. Pea protein includes four major classes (globulin, albumin, prolamin, and glutelin), in which globulin and albumin are major storage proteins in pea seeds. Globulin is soluble in salt solutions and can be further classified into legumin and vicilin. Albumin is soluble in water and regarded as metabolic and enzymatic proteins with cytosolic functions. Pea protein has a well-balanced amino acid profile with high level of lysine. The composition and structure of pea protein, as well as the processing conditions, significantly affect its physical and chemical properties, such as hydration, rheological characteristics, and surface characteristics. With its availability, low cost, nutritional values and health benefits, pea protein can be used as a novel and effective alternative to substitute for soybean or animal proteins in functional food applications.
Confidence predicts speed-accuracy tradeoff for subsequent decisions

When external feedback about decision outcomes is lacking, agents need to adapt their decision policies based on an internal estimate of the correctness of their choices (i.e., decision confidence). We hypothesized that agents use confidence to continuously update the tradeoff between the speed and accuracy of their decisions: When confidence is low in one decision, the agent needs more evidence before committing to a choice in the next decision, leading to slower but more accurate decisions. We tested this hypothesis by fitting a bounded accumulation decision model to behavioral data from three different perceptual choice tasks. Decision bounds indeed depended on the reported confidence on the previous trial, independent of objective accuracy. This increase in decision bound was predicted by a centro-parietal EEG component sensitive to confidence. We conclude that internally computed neural signals of confidence predict the ongoing adjustment of decision policies.
Evaluating the Bioactivity of a Novel Antimicrobial and Anticancer Peptide, Dermaseptin-PS4(Der-PS4), from the Skin Secretion of Phyllomedusa sauvagii

Dermaseptins belonging to a large family of cationic membrane-disruption antimicrobial peptides display extensive antibacterial and antiproliferative activities depending on a coil-to-helix transition and the specific structural parameters. Herein, a novel dermaseptin peptide named Der-PS4 was discovered from the skin secretion of the waxy monkey tree frog, Phyllomedusa sauvagii. The complementary DNA (cDNA)-encoding precursor was obtained relying on “shotgun” cloning, and afterwards, a mature peptide amino acid sequence was identified by reverse-phase high performance liquid chromatography (RP-HPLC) and MS/MS. Specimens were chemically synthesized and applied for further functional studies. Structural analysis demonstrated a higher α-helical content in the membrane-mimetic environment compared with that in the ammonium acetate/water circumstance. Der-PS4 displayed a broad spectrum of antimicrobial activities against tested pathogenic microorganisms, however, exhibiting slight membrane-damaging effectiveness towards horse red blood cells. Coincident with the inhibitory activities on pathogens, Der-PS4 also showed considerable biofilm eradicating impact. Also, Der-PS4 penetrated cell membrane in a relative short period under each minimum bactericidal concentration. In addition, Der-PS4 possessed antiproliferative capacity against five cancer cell lines, while presenting slight suppressing effect on human microvascular endothelial, HMEC-1. These findings provide a promising insight for the discovery and development of novel drugs from a natural source.
A 5Ad Dietary Protocol for Functional Bowel Disorders

Functional bowel disorders (FBDs) affect around 20% of the population worldwide and are associated with reduced quality of life and high healthcare costs. Dietary therapies are frequently implemented to assist with symptom relief in these individuals, however, there are concerns regarding their complexity, restrictiveness, nutritional adequacy, and effectiveness. Thus, to overcome these limitations, a novel approach, the 5Ad Dietary Protocol, was designed and tested for its efficacy in reducing the severity of a range of gastrointestinal symptoms in 22 subjects with FBDs. The protocol was evaluated in a repeated measures MANOVA design (baseline week and intervention week). Measures of stool consistency and frequency were subtyped based on the subject baseline status. Significant improvements were seen in all abdominal symptom measures (p < 0.01). The effect was independent of body mass index (BMI), age, gender, physical activity level, and whether or not the subjects were formally diagnosed with irritable bowel syndrome (IBS) prior to participation. Stool consistency and frequency also improved in the respective contrasting subtypes. The 5Ad Dietary Protocol proved to be a promising universal approach for varying forms and severities of FBDs. The present study paves the way for future research encompassing a longer study duration and the exploration of underlying physiological mechanisms.
Improving HIV Surveillance Data by Using the ATra Black Box System to Assist Regional Deduplication Activities.

BACKGROUND Focused attention on Data to Care underlines the importance of high-quality HIV surveillance data. This study identified the number of total duplicate and exact duplicate HIV case records in 9 separate Enhanced HIV/AIDS Reporting System (eHARS) databases reported by 8 jurisdictions and compared this approach to traditional Routine Interstate Duplicate Review resolution. METHODS This study used the ATra Black Box System and 6 eHARS variables for matching case records across jurisdictions: last name, first name, date of birth, sex assigned at birth (birth sex), social security number, and race/ethnicity, plus 4 system-calculated values (first name Soundex, last name Soundex, partial date of birth, and partial social security number). RESULTS In approximately 11 hours, this study matched 290,482 cases from 799,326 uploaded records, including 55,460 exact case pairs. Top case pair overlaps were between NYC and NYS (51%), DC and MD (10%), and FL and NYC (6%), followed closely by FL and NYS (4%), FL and NC (3%), DC and VA (3%), and MD and VA (3%). Jurisdictions estimated that they realized a combined 135 labor hours in time efficiency by using this approach compared with manual methods previously used for interstate duplication resolution. DISCUSSION This approach discovered exact matches that were not previously identified. It also decreased time spent resolving duplicated case records across jurisdictions while improving accuracy and completeness of HIV surveillance data in support of public health program policies. Future uses of this approach should consider standardized protocols for postprocessing eHARS data.
Effects of oxygen-glucose deprivation (OGD) on barrier properties and mRNA transcript levels of selected marker proteins in brain endothelial cells/astrocyte co-cultures

Ischemic stroke has been shown to induce breakdown of the blood-brain barrier, although these changes are not fully characterized. Oxygen-glucose deprivation (OGD) has been used to investigate the effects of ischemia in cultured brain capillary endothelial cells, however this involves a change of medium which in itself may affect the cells. The aim of the present study was to investigate the effect of OGD and simple medium exchange followed by 48 h of reperfusion on barrier properties of primary bovine endothelial cells co-cultured with rat astrocytes. Barrier properties were evaluated by transendothelial electrical resistance measurements, passive permeability of flux markers, RT-qPCR and immunocytochemistry. Both OGD and simple medium exchange caused an increase in endothelial monolayer permeability. This correlated with reduced transcript levels of a number of tight junction and tight junction-associated proteins (claudin-1, claudin-5, occludin, ZO-1, tricellulin, marveld3 and PECAM-1), as well as with altered transcript level of several transporters and receptors (GLUT-1, HB-EGF, InsR, TfR, two members of the low density lipoprotein receptor family, LDLR and LRP-1, and the efflux transporter BCRP). In contrast, effects induced specifically by OGD were transient de-localization of claudin-5 from the junction zone, increased InsR localization at the plasma membrane and transient downregulation of MRP-1 and P-gp transcript levels. In conclusion, OGD caused changes in claudin-5 and InsR localization, as well as in MRP-1 and P-gp transcript levels. Our results however also indicated that medium exchange alone caused changes in functional barrier properties and expression levels of wide range of proteins.
A real-space based benchmark of G0W0 calculations on GW100: effects of semi-core orbitals and orbital reordering.

Using an implementation based on real-space wave functions, we perform converged G0W0 calculations of the HOMO and LUMO energies of molecules and atoms in the GW100 set. Our main conclusions are: (1). Different implementations of the G0W0 approximation show better agreements for HOMO (highest occupied molecular orbital) energies than for LUMO (lowest unoccupied molecular orbital) energies. The mean absolute differences for all molecules and atoms in the GW100 set between pseudopotential codes range from 100 to 200 meV. For delocalized LUMOs, all-electron codes tend to predict much higher energies than those calculated with pseudopotential codes. (2). The role of semi-core electrons in pseudopotentials can explain some of the large discrepancies. For molecules or atoms that includes I, Xe, and Ga, exclusion of semi-core electrons produces results that agree better with all-electron calculations. For polar molecules such as NaCl and BrK, however, it is necessary to include semi-core electrons for alkaline metal elements to get correct LUMO energies. (3). 22 molecules show rearrangement of the order between LUMO (or HOMO) with other orbitals due to GW corrections. The predicted LUMO GW levels (or electron affinity) can be corrected by 2.0 eV if we consider the rearrangement of orbitals in GW calculations. In all, our work clarifies some of the discrepancies between different GW codes and sets a benchmark for real-space implementations of the G0W0 approximation.
Stochastic Variance Reduced Gradient for affine rank minimization problem

We develop an efficient stochastic variance reduced gradient descent algorithm to solve the affine rank minimization problem consists of finding a matrix of minimum rank from linear measurements. The proposed algorithm as a stochastic gradient descent strategy enjoys a more favorable complexity than full gradients. It also reduces the variance of the stochastic gradient at each iteration and accelerate the rate of convergence. We prove that the proposed algorithm converges linearly in expectation to the solution under a restricted isometry condition. The numerical experiments show that the proposed algorithm has a clearly advantageous balance of efficiency, adaptivity, and accuracy compared with other state-of-the-art greedy algorithms.
Image Representations With Spatial Object-to-Object Relations for RGB-D Scene Recognition

Scene recognition is challenging due to the intra-class diversity and inter-class similarity. Previous works recognize scenes either with global representations or with the intermediate representations of objects. In contrast, we investigate more discriminative image representations of object-to-object relations for scene recognition, which are based on the triplets of obtained with detection techniques. Particularly, two types of representations, including co-occurring frequency of object-to-object relation (denoted as COOR) and sequential representation of object-to-object relation (denoted as SOOR), are proposed to describe objects and their relative relations in different forms. COOR is represented as the intermediate representation of co-occurring frequency of objects and their relations, with a three order tensor that can be fed to scene classifier without further embedding. SOOR is represented in a more explicit and freer form that sequentially describe image contents with local captions. And a sequence encoding model (e.g., recurrent neural network (RNN)) is implemented to encode SOOR to the features for feeding the classifiers. In order to better capture the spatial information, the proposed COOR and SOOR are adapted to RGB-D data, where a RGB-D proposal fusion method is proposed for RGB-D object detection. With the proposed approaches COOR and SOOR, we obtain the state-of-the-art results of RGB-D scene recognition on SUN RGB-D and NYUD2 datasets.
Racial/ethnic, age and sex disparities in leukemia survival among adults in the United States during 1973-2014 period

There has been marked improvement in leukemia survival, particularly among children in recent time. However, the long-term trends in survival among adult leukemia patients and the associated sex and racial survival disparities are not well understood. We, therefore, evaluated the secular trends in survival improvement of leukemia patients from 1973 through 2014, using Surveillance Epidemiology and End-Result Survey Program (SEER) data. ICD-O-3 morphology codes were used to group leukemia into four types: acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), chronic myeloid leukemia (CML). Survival analysis for each leukemia type stratified by race/ethnicity, age, sex was performed to generate relative survival probability estimates for the baseline time period of 1973 through 1979. Hazard ratios (HR) and respective 95% confidence intervals (CIs) for survival within subsequent 10-year time periods by race, age and sex were calculated using Cox proportional hazard models. Of the 83,255 leukemia patients for the current analysis, the 5-year survival of patients with ALL, AML, CLL, and CML during 1973–1979 were 42.0%, 6.5%, 66.5%, and 20.9%, respectively. Compared to the baseline, there were substantial improvements of leukemia-specific survival in 2010–2014 among African-American (81.0%) and Asian (80.0%) patients with CML and among 20–49 year of age with CLL (96.0%). African-American patients, those with AML and those older than 75 years of age had the lowest survival improvements. Asians experienced some of the largest survival improvements during the study period. Others, including African-American and the elderly, have not benefited as much from advances in leukemia treatment.
Influence of Striatal Dopamine, Cerebral Small Vessel Disease, and Other Risk Factors on Age-Related Parkinsonian Motor Signs.

OBJECTIVE Parkinsonian motor signs are common and disabling in older adults without Parkinson's disease (PD), but its risk factors are not completely understood. We assessed the influence of striatal dopamine levels, cerebral small vessel disease, and other factors on age-related parkinsonian motor signs in non-PD adults. METHODS Striatal dopamine transporter (DAT) binding was quantified via [11C]-CFT positron emission tomography in 87 neurologically intact adults (20-85 years, 57.47% female) with concurrent data on: Unified Parkinson's Disease Rating Scale motor (UPDRSm), white matter hyperintensities (WMH), and other risk factors (grip strength, vibratory sensitivity, cardio- and cerebro-vascular comorbidities). Sex-adjusted nonparametric models first estimated the associations of age, DAT, WMH, and other factors with UPDRSm; next, interactions of age by DAT, WMH, or other factors were tested. To quantify the influence of DAT, WMH, and other risk factors on the main association of age with UPDRSm, multivariable mediation models with bootstrapped confidence intervals (CI) were used. RESULTS Older age, lower DAT, higher WMH, and worse risk factors significantly predicted worse UPDRSm (sex-adjusted p < .04 for all). DAT, but not WMH or other factors, positively and significantly interacted with age (p = .02). DAT significantly reduced the age-UPDRSm association by 30% (results of fully adjusted mediation model: indirect effect: 0.027; bootstrapped 95% CI: 0.0007, 0.074). CONCLUSIONS Striatal dopamine appears to influence to some extent the relationship between age and parkinsonian signs. However, much of the variance of parkinsonian signs appears unexplained. Longitudinal studies to elucidate the multifactorial causes of this common condition of older age are warranted.
Imbalance of Pro- and Anti-Angiogenic Factors Due to Maternal Vitamin D Deficiency Causes Renal Microvasculature Alterations Affecting the Adult Kidney Function

Vitamin D (Vit.D) is involved in cellular proliferation and differentiation and regulation of the renin gene, which are important aspects of nephrogenesis and quiescence of renal health in adulthood. This study evaluated the angiogenic mechanisms involved in long term renal disturbances induced by Vit.D deficiency persistent in adulthood in rats. First-generation male Hannover offspring from mothers fed either a control diet (control group, CG) or Vit.D-deficient diet (Vit.D- group) were evaluated. Systolic blood pressure (SBP) was measured monthly during the first 6 months after birth, and blood and urine samples were collected to evaluate renal function. Nitric oxide (NO), angiotensin II (ANGII), parathyroid hormone (PTH), calcium, and Vit.D were measured. The kidneys were then removed for morphometric, NO, immunohistochemical, and Western blot studies. We evaluated the expression of vascular growth factor (VEGF) and angiopoietins 1 and 2 and their receptors since this intrinsic renal axis is responsible for endothelial quiescence. Compared to CG, the Vit.D- group presented higher SBP, ANG II plasma levels, renin expression, and AT1 receptor expression levels. Capillary rarefaction was observed, as well as an imbalance between pro- and anti-angiogenic factors. Collectively, the present findings support the role of Vit.D for maintaining the integrity of renal microcirculation.