Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct Laser Patterning and Phase Transformation of 2D PdSe2 Films for On-Demand Device Fabrication.

Heterophase homojunction formation in atomically thin 2D layers is of great importance for next-generation nanoelectronics and optoelectronics applications. Technologically challenging, controllable transformation between the semiconducting and metallic phases of transition metal chalcogenides is of particular importance. Here, we demonstrate that controlled laser irradiation can be used to directly ablate PdSe2 thin films using high power or trigger the local transformation of PdSe2 into a metallic phase PdSe2-x using lower laser power. Such transformations are possible due to the low decomposition temperature of PdSe2 and a variety of stable phases compared to other 2D transition metal dichalcogenides. Scanning transmission electron microscopy is used to reveal the laser-induced Se-deficient phases of PdSe2 material. The process sensitivity to the laser power allows patterning flexibility for resist-free device fabrication. The laser-patterned devices demonstrate that a laser-induced metallic phase PdSe2-x is stable with increased conductivity by a factor of about 20 compared to PdSe2. These findings contribute to the development of nanoscale devices with homojunctions and scalable methods to achieve structural transformations in 2D materials.
Maternal cumulative exposure to extremely low frequency electromagnetic fields, prematurity and small for gestational age: a pooled analysis of two birth cohorts

Background Data on the effects of extremely low frequency electromagnetic fields (ELF-EMF) on pregnancy outcomes are inconclusive. Objective To study the relation between maternal cumulative exposure to ELF-EMF during pregnancy and the risk of prematurity or small for gestational age (SGA) in a pooled analysis of two French birth cohorts. Methods Elfe and Epipage2 are both population-based birth cohorts initiated in 2011 and included 18 329 and 8400 births, respectively. Health data and household, mother and child characteristics were obtained from medical records and questionnaires at maternity and during follow-up. A job exposure matrix was used to assess cumulative exposure to ELF-EMF during three periods: (1) until 15 weeks of gestation, (2) until 28 weeks of gestation and (3) until 32 weeks of gestation. Analyses were restricted to single live births in mainland France and to mothers with documented jobs (N=19 894). Adjusted logistic regression models were used. Results According to the period studied, 3.2%–4% of mothers were classified as highly exposed. Results were heterogeneous. Increased risks of prematurity were found among low exposed mothers for the three periods, and no association was observed among the most exposed (OR1=0.92 (95% CI 0.74 to 1.15); OR2=0.98 (95% CI 0.80 to 1.21); OR3=1.14 (95% CI 0.92 to 1.41)). For SGA, no association was observed with the exception of increased risk among the low exposed mothers in period 2 and the most exposed in period 3 (OR=1.25 (95% CI 1.02 to 1.53)). Conclusion Some heterogeneous associations between ELF-EMF exposure and prematurity and SGA were observed. However, due to heterogeneity (ie, their independence regarding the level of exposure), associations cannot be definitely explained by ELF-EMF exposure.
Modification of NaY zeolite by lanthanum and hexadecyl trimethyl ammonium bromide and its removal performance for nitrate

Nitrate in the effluent of wastewater treatment plants (WWTPs) is the main nitrogen resource in natural water. The excessive nitrogen in natural water causes ecological issues such as aqueous eutrophication. A novel modified NaY zeolite (SMZ‐La) with hexadecyl trimethyl ammonium bromide (HDTMA) and lanthanum (La) as modifying agents for NO3- ‐N adsorption was investigated in this study. Results showed that SMZ‐La had a higher adsorption capacity (3.82 mg NO3- ‐N/g) than zeolite only modified with HDTMA or La (2.75 and 2.23 mg NO3- ‐N/g, respectively). Moreover, the adsorption process was endothermic with a maximum theoretic adsorption of 14.49 mg NO3- ‐N/g. X‐ray photoelectron spectroscopy (XPS) analysis indicated that adsorption rate principally depended on chemisorption between SMZ and NO3- ‐N. Thermogravimetric analysis showed that HDTMA was loaded on the surface of NaY zeolite with double layer. Scanning electron microscope and X‐ray spectroscopy analysis illustrated that La was primarily loaded in the pore of NaY zeolite, and the loading of HDTMA and La did not affect the original crystal structure of NaY zeolite. The novel adsorbent provided a promising perspective for nitrogen control in WWTPs and natural water.
Association Between Dietary Nutrient Intake and Chronic Obstructive Pulmonary Disease Severity: A Nationwide Population-Based Representative Sample

Abstract Several nutrients have been suggested to protect against airway destruction via antioxidant activity. The present study aimed to evaluate the association between disease severity and dietary nutrient intake in chronic obstructive pulmonary disease (COPD) patients using the Korea National Health and Nutrition Examination Survey. Of the 22,948 participants, 702 patients (418 men and 284 women) with COPD, who were defined as the fifth percentile from a reference population were selected. The severity of airflow limitation was measured by the predicted percentage of forced expiratory volume in 1 second (FEV1%). The Jonckheere–Terpstra test was used to evaluate the dose-dependent association between nutrient intake and disease severity. Multivariate linear regression analysis was used to evaluate the relationship between dietary nutrient intake and predicted FEV1%. Vitamin A intake showed a positive association with FEV1% in men in a model adjusted for covariates. Carbohydrate, protein, fiber, thiamin, riboflavin, niacin, and vitamin C intake were significantly associated with decreased disease severity in elderly men (aged ≥60 years). On the contrary, statistical significance was not observed for all the nutrients in women. In conclusion, intake of carbohydrate, protein, fiber, thiamin, riboflavin, niacin, and vitamin C was associated with decreased severity of airway impairment in elderly men with COPD. Our results are in line with those of previous studies into the importance of nutritional status in airway disease. A longitudinal study is required to clarify the mechanisms underlying the association between dietary nutrient intake and COPD severity.
Masked form priming as a function of letter position: An evaluation of current orthographic coding models.

A word's exterior letters, particularly its initial letter, appear to have a special status when reading. Therefore, most orthographic coding models incorporate assumptions giving initial letters and, in some cases, final letters, enhanced importance during the orthographic coding process. In the present article, 3 masked priming experiments were carried out, using the conventional lexical-decision task, the sandwich priming lexical-decision task and the masked priming same-different task, in an attempt to examine a number of those models with a specific focus on the implications of the models' assumptions concerning the different letter positions. The related primes and targets were 6-letter strings that differed in 2 letter positions, initial (e.g., jnckey-HOCKEY), middle (e.g., hojney-HOCKEY), or final (hockjn-HOCKEY), with the middle-letters different primes being the primes that maintained both end letters. To the extent possible, the predictions of the models were derived by using easyNet, the simulation program recently developed by Adelman, Gubian, and Davis (2017). In all experiments, the final-letters different primes were the most effective primes with there being no clear distinction between the other 2 prime types, a pattern that none of the models predicted. The lack of an advantage for the middle-letters different primes suggests that the orthographic code driving masked priming is not one that places a special emphasis on the identities of the exterior letters. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
The Longitudinal Impact of Excessive Daytime Somnolence on Motor and Nonmotor Symptoms of Parkinson's Disease in a Southeast Asian Cohort

Objective: Sleep–wake disturbances, such as excessive daytime somnolence (EDS), are nonmotor symptoms of Parkinson's disease (PD) and significantly affect the quality of life. This study aimed to examine the relationship between EDS and motor and nonmotor symptoms of PD. Methods: Eighty-two patients with idiopathic mild PD were followed up twice a year for 2 years and assessed on sleep, mood, anxiety, cognition, function, and disease severity. Data were analyzed retrospectively, comparing motor and nonmotor outcomes between those with EDS and those without. Results: At baseline, 27.9% had EDS and were similar in demographic and clinical characteristics to those without; 10% had persistent EDS during the first year of follow-up. Excessive daytime somnolence had a significant main effect on mood and anxiety as shown by consistently higher scores on the Geriatric Depression Scale (P = .022) and Hospital Anxiety and Depression Scale-Anxiety subscale scores (P = .011) throughout duration of follow-up. The group with persistent EDS showed greater rate of worsening Frontal Assessment Battery scores by the end of first-year follow-up (P = .025) and greater rate of worsening Apathy Scale scores by the end of 2-year follow-up (P = .002). No significant effects of EDS on motor symptoms and disease severity were found. Conclusions: In a Southeast Asian cohort of patients with PD, EDS had a negative longitudinal impact on mood, anxiety, apathy, and cognitive function but no impact on motor symptoms and disease severity. Excessive daytime somnolence is thus a potential therapeutic target to improve nonmotor outcomes.
Single-cell and spatial transcriptomics approaches of the bone marrow microenvironment.

PURPOSE OF REVIEW The bone marrow is home to hematopoietic stem cells responsible for lifelong blood production, alongside mesenchymal stem cells required for skeletal regeneration. In the bone marrow, a unique combination of signals derived from a multitude of cell types results in the establishment of so-called niches that regulate stem-cell maintenance and differentiation. Recently, single-cell and spatially resolved transcriptomics technologies have been utilized to characterize the murine bone marrow microenvironment during homeostasis, stress and upon cancer-induced remodeling. In this review, we summarize the major findings of these studies. RECENT FINDINGS Single-cell technologies applied to bone marrow provided the first systematic and label-free identification of bone marrow cell types, enabled their molecular and spatial characterization, and clarified the cellular sources of key prohematopoietic factors. Large transcriptional heterogeneity and novel subpopulations were observed in compartments previously thought to be homogenous. For example, Lepr Cxcl12-abundant reticular cells were shown to constitute the major source of prohematopoietic factors, but consist of subpopulations differing in their adipogenic versus osteogenic priming, morphology and localization. These subpopulations were suggested to act as professional cytokine secreting cells, thereby establishing distinct bone marrow niches. SUMMARY Single-cell and spatially resolved transcriptomics approaches have clarified the molecular identity and localization of bone marrow-resident cell types, paving the road for a deeper exploration of bone marrow niches in the mouse and humans.
Proteomes of the past: the pursuit of proteins in paleontology

ABSTRACT Introduction: Despite an extensive published literature, skepticism over the claim of original biochemicals including proteins preserved in the fossil record persists and the issue remains controversial. Workers using many different techniques including mass spectrometry, X-ray, electron microscopy and optical spectroscopic techniques, have attempted to verify proteinaceous or other biochemicals that appear endogenous to fossils found throughout the geologic column. Areas covered: This paper presents a review of the relevant literature published over the last 50 years. A comparative survey of the reported techniques used is also given. Expert opinion: Morphological and molecular investigations show that original biochemistry is geologically extensive, geographically global, and taxonomically wide-ranging. The survival of endogenous organics in fossils remains the subject of widespread and increasing research investigation.
Effects of Physical Activity on Neurophysiologic and Gene Expression Profiles in Chronic Back Pain: Study Protocol.

BACKGROUND Despite the emphasis on exercise to reduce pain and improve function among people with chronic low back pain (cLBP), little is known about the underlying mechanism of the impact of exercise on the neurophysiologic and gene transcription alterations that characterize cLBP. OBJECTIVES To present a study protocol to examine the feasibility, acceptability, and initial efficacy of Problem-solving Pain to Enhance Living Well (PROPEL) with the support of nurse consultations and wearable activity tracking technology on self-management (SM) knowledge, skills, physical activity, and pain and to examine the differential neurophysiologic and gene expression profiles in cLBP participants from pre- to post-PROPEL. METHODS A pretest and posttest study is employed on 40 adults ages 18-60 with cLBP who do not have serious complications and/or comorbidities that affect sensorimotor function. Participants will receive video modules focused on SM and biweekly phone consultations to facilitate symptom monitoring and problem-solving while increasing physical activity frequency and duration. Participants will be assessed for outcomes including SM skills, physical activity, and pain every 2 weeks for 12 weeks. We will examine the participants' differential neurophysiologic and gene expression profiles at 12 weeks post-intervention and correlate these outcomes with the total duration of physical activity. RESULTS The study began in September 2018. Of the 99 subjects that were screened, 23 were enrolled, and 8 completed data collection. DISCUSSION Comparing the neurophysiologic and gene expression profiles of people with cLBP exposed to PROPEL could inform the development of interventions that offer personalized physical activity dosage along with general SM support. Web-based programs such as PROPEL have the potential to enhance accessibility of evidence-based interventions that improve functionality and quality of life among people living with cLBP.
What impact do Rome IV criteria have on patients with IBS in China?

Abstract Background: The Rome criteria for functional gastrointestinal diseases (FGIDs) have been updated from Rome III to Rome IV. This study aimed to investigate the impact of the update on patients with irritable bowel syndrome (IBS) in China. Methods: A previous database including consecutive patients with FGIDs (according to Rome III criteria) from gastrointestinal department of a tertiary hospital in China was re-analyzed. Demographic information, clinical symptoms, psychological status (Zung self-rating scale), and sleep quality (Pittsburgh sleep quality index) were compared between patients with Rome III and Rome IV IBS. Results: Of the 946 patients with FGIDs, only 58 (6.1%) were diagnosed with Rome IV IBS [less than 292 (30.9%) under Rome III criteria] with a surge of the number of unspecified functional bowel disorders (U-FBD). All patients with IBS were divided into three groups: group A [meeting both Rome III and IV criteria, accounting for 43 (4.6%) of patients with FGIDs], group B [meeting only Rome III criteria, 249 (26.3%)], and group C [meeting only Rome IV criteria,15 (1.6%)]. Significant differences in frequency and severity of symptoms, subtypes, and sleep quality among groups (all p < .05) were found. Patients with Rome III IBS having sleep disorder tended to be more serious than those without. On the contrary, it was not the case under Rome IV criteria. Conclusions: Number of IBS patients was greatly reduced accompanied by a surge in U-FBD. Besides, the updated criteria also had great impacts on clinical parameters, sleep quality and psychological state of IBS patients. Highlights Rome IV criteria removed the description of abdominal discomfort for IBS. The updated Rome criteria had great impacts on IBS patients in our database. Our study analyzed the characteristics of IBS patients who fulfilled both criteria. Alterations in the Rome criteria also led to changes in the disease spectrum of FBD.
Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif

Endolithic microbial communities survive nutrient and energy deficient conditions while contributing to the weathering of their mineral substrate. This study examined the mineral composition and microbial communities of fully serpentinized weathered rock from 0.1 to 6.5 m depth at a site within the Khalilovsky massif, Orenburg Region, Southern Ural Mountains, Russia. The mineral composition includes a major content of serpentinite family (mostly consisting of lizardite and chrysotile), magnesium hydrocarbonates (hydromagnesite with lesser amounts of hydrotalcite and pyroaurite) concentrated in the upper layers, and clay minerals. We found that the deep-seated weathered serpentinites are chrysotile-type minerals, while the middle and surface serpentinites mostly consist of lizardite and chrysotile types. Microbial community analysis, based on 16S rRNA gene sequencing, showed a similar diversity of phyla throughout the depth profile. The dominant bacterial phyla were the Actinobacteria (of which unclassified genera in the orders Acidimicrobiales and Actinomycetales were most numerous), Chloroflexi (dominated by an uncultured P2-11E order) and the Proteobacteria (predominantly class Betaproteobacteria). Densities of several groups of bacteria were negatively correlated with depth. Occurrence of the orders Actinomycetales, Gaiellales, Solirubrobacterales, Rhizobiales and Burkholderiales were positively correlated with depth. Our findings show that endolithic microbial communities of the Khalilovsky massif have similar diversity to those of serpentine soils and rocks, but are substantially different from those of the aqueous environments of actively serpentinizing systems.
dSreg: a Bayesian model to integrate changes in splicing and RNA-binding protein activity

Alternative splicing (AS) is an important mechanism in the generation of the great transcript diversity found across mammals. AS patterns are dynamically regulated during development and in response to environmental changes. Defects or perturbations in their regulation system may lead to cardiac or neuro-logical disorders. These regulatory mechanisms are typically inferred using a two step-framework: differential AS analysis followed by enrichment methods. These strategies require setting rather arbitrary thresholds and are prone to error propagation between steps. Here, we examined the influence of different sequencing depths in the identification of regulatory patterns of AS using simulated data with traditional workflows, showing poor performance and high dependence on sequencing depth. We developed a bayesian model that integrates RNA-seq and regulatory elements data to simultaneously infer changes in inclusion rates and in the activity of the underlying regulators. This model pools weak evidence across AS events to increase the power to infer changes in the regulatory activity using binding sites information increasing both sensitivity and specificity on simulated data. Application to a real dataset provided new insights into the underlying regulatory mechanisms of AS changes, proving the usefulness of our approach for future studies and reanalyses. dSreg was implemented in python using stan and is freely available to the community at https://bitbucket.org/cmartiga/pydsreg/src/master/.
Apolipoprotein B, Triglyceride-Rich Lipoproteins, and Risk of Cardiovascular Events in Persons with CKD.

BACKGROUND AND OBJECTIVES Triglyceride-rich lipoproteins may contribute to the high cardiovascular risk of patients with CKD. This study evaluated associations of apo-B and markers of triglyceride-rich lipoproteins with cardiovascular events in people with CKD. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Analyses were conducted in 9270 participants with CKD in the Study of Heart and Renal Protection (SHARP): 6245 not on dialysis (mean eGFR 26.5 ml/min per 1.73 m2), and 3025 on dialysis when recruited. Cox regression methods were used to evaluate associations of lipids with incident atherosclerotic and nonatherosclerotic vascular events, adjusting for demographics and clinical characteristics. Hazard ratios (HRs) were calculated per 1 SD higher level for apo-B, HDL cholesterol, LDL cholesterol, triglyceride-rich lipoprotein cholesterol (i.e., total cholesterol minus LDL cholesterol minus HDL cholesterol), non-HDL cholesterol, log triglyceride, and log ratio of triglyceride to HDL cholesterol. RESULTS During a median follow-up of 4.9 years (interquartile range, 4.0-5.5 years), 1406 participants experienced at least one atherosclerotic vascular event. In multivariable adjusted models, positive associations with atherosclerotic vascular events were observed for apo-B (HR per 1 SD, 1.19; 95% confidence interval, 1.12 to 1.27), triglycerides (1.06; 1.00 to 1.13), the ratio of triglyceride to HDL cholesterol (1.10; 1.03 to 1.18), and triglyceride-rich lipoprotein cholesterol (1.14; 1.05 to 1.25). By contrast, inverse associations with nonatherosclerotic vascular events were observed for each of these lipid markers: apo-B (HR per 1 SD, 0.92; 0.85 to 0.98), triglycerides (0.86; 0.81 to 0.92), the ratio of triglyceride to HDL cholesterol (0.88; 0.82 to 0.94), and triglyceride-rich lipoprotein cholesterol (0.85; 0.77 to 0.94). CONCLUSIONS Higher apo-B, triglycerides, ratio of triglyceride to HDL cholesterol, and triglyceride-rich lipoprotein cholesterol concentrations were associated with increased risk of atherosclerotic vascular events in CKD. Reducing triglyceride-rich lipoproteins using novel therapeutic agents could potentially lower the risk of atherosclerotic cardiovascular disease risk in the CKD population.
Good, better, best: clinical scenarios for the use of L-methylfolate in patients with MDD

Abstract Depression is among the most prevalent mental disorders worldwide, and a substantial proportion of patients do not respond adequately to standard antidepressants. Our understanding of the pathophysiology of depression is no longer limited to the chemical imbalance of neurotransmitters, but also involves the interplay of proinflammatory modulators in the central nervous system, as well as folate metabolism. Additional factors such as stress and metabolic disorders also may contribute. Multiple inflammatory, metabolic, and genetic markers have been identified and may provide critical information to help clinicians individualize treatments for patients to achieve optimal outcomes. Recent advancements in research have clarified underlying causes of depression and have led to possible new avenues for adjunctive treatment. Among these is L-methylfolate, a medical food that is thought to enhance synthesis of monoamines (serotonin, norepinephrine, and dopamine), suppress inflammation, and promote neural health. Clinical studies that assessed supplemental use of L-methylfolate in patients with usual care-resistant depression found that it resulted in improved outcomes. Patients with selective serotonin reuptake inhibitor-resistant depression, and particularly subgroups with biomarkers of inflammation or metabolic disorders or folate metabolism-related genetic polymorphisms (or ≥2 of these factors), had the best responses. Considering this, the goals of this review are to 1) highlight recent advances in the pathophysiology of major depressive disorder as it pertains to folate and associated biomarkers and 2) establish the profiles of patients with depression who could benefit most from supplemental use of L-methylfolate.