julilili42/papers huggingface dataset:
Inferring interpretable dynamical generators of local quantum observables from projective measurements through machine learning
2024-04-03

To characterize the dynamical behavior of many-body quantum systems, one is usually interested in the evolution of so-called order parameters rather than in characterizing the full quantum state. In many situations, these quantities coincide with the expectation value of local observables, such as the magnetization or the particle density. In experiment, however, these expectation values can only be obtained with a finite degree of accuracy due to the effects of the projection noise. Here, we utilize a machine-learning approach to infer the dynamical generator governing the evolution of local observables in a many-body system from noisy data. To benchmark our method, we consider a variant of the quantum Ising model and generate synthetic experimental data, containing the results of N projective measurements at M sampling points in time, using the time-evolving block-decimation algorithm. As we show, across a wide range of parameters the dynamical generator of local observables can be approximated by a Markovian quantum master equation. Our method is not only useful for extracting effective dynamical generators from many-body systems but may also be applied for inferring decoherence mechanisms of quantum simulation and computing platforms.
The genetic basis of early-onset hereditary ataxia in Iran: results of a national registry of a heterogeneous population
2024-04-03

Abstract Background To investigate the genetics of early-onset progressive cerebellar ataxia in Iran, we conducted a study at the Children’s Medical Center (CMC), the primary referral center for pediatric disorders in the country, over a three-year period from 2019 to 2022. In this report, we provide the initial findings from the national registry. Methods We selected all early-onset patients with an autosomal recessive mode of inheritance to assess their phenotype, paraclinical tests, and genotypes. The clinical data encompassed clinical features, the Scale for the Assessment and Rating of Ataxia (SARA) scores, Magnetic Resonance Imaging (MRI) results, Electrodiagnostic exams (EDX), and biomarker features. Our genetic investigations included single-gene testing, Whole Exome Sequencing (WES), and Whole Genome Sequencing (WGS). Results Our study enrolled 162 patients from various geographic regions of our country. Among our subpopulations, we identified known and novel pathogenic variants in 42 genes in 97 families. The overall genetic diagnostic rate was 59.9%. Notably, we observed PLA2G6 , ATM , SACS , and SCA variants in 19, 14, 12, and 10 families, respectively. Remarkably, more than 59% of the cases were attributed to pathogenic variants in these genes. Conclusions Iran, being at the crossroad of the Middle East, exhibits a highly diverse genetic etiology for autosomal recessive hereditary ataxia. In light of this heterogeneity, the development of preventive strategies and targeted molecular therapeutics becomes crucial. A national guideline for the diagnosis and management of patients with these conditions could significantly aid in advancing healthcare approaches and improving patient outcomes.
Deferred Tax Asset Revaluations, Costly Information Processing, and Bank Deposits: Evidence from the Tax Cuts and Jobs Act
2024-04-03

We examine how information processing costs affect the extent to which depositors’ use the details in banks’ income statements. Depositors have a unique cost-benefit structure because they are nonprofessional users of financial information and have high information processing costs. At the same time, they benefit from acting quickly because failing banks make payments on a first-come, first-serve basis. This makes it likely that they will react to a prominent summary measure like the reported net income without adjusting for any risk-irrelevant information included in the line items. In our empirical analysis, we investigate depositors’ behavior as driven by the mechanical revaluations of deferred tax assets due to the 2017 Tax Cuts and Jobs Act. Using a difference-in-difference design, we find deposit withdrawals because of this risk-irrelevant information. In cross-sectional tests, we show that the withdrawals are stronger if the information acquisition costs are low, and the information integration costs are high. Overall, our results show that information processing costs are important for understanding depositors’ reactions to accounting information and can lead to deposit flows that cannot be explained by new risk-relevant information. This paper was accepted by Brian Bushee, accounting. Funding: We kindly acknowledge funding by the Werner Diez Foundation [Grant 2024.1] to make this work available under a Creative Commons license. Supplemental Material: The online appendix and data files are available at https://doi.org/10.1287/mnsc.2022.03176 .
Human CRB1 and CRB2 form homo- and heteromeric protein complexes in the retina
2024-04-03

Crumbs homolog 1 ( CRB1 ) is one of the key genes linked to retinitis pigmentosa and Leber congenital amaurosis, which are characterized by a high clinical heterogeneity. The Crumbs family member CRB2 has a similar protein structure to CRB1, and in zebrafish, Crb2 has been shown to interact through the extracellular domain. Here, we show that CRB1 and CRB2 co-localize in the human retina and human iPSC-derived retinal organoids. In retina-specific pull-downs, CRB1 was enriched in CRB2 samples, supporting a CRB1–CRB2 interaction. Furthermore, novel interactors of the crumbs complex were identified, representing a retina-derived protein interaction network. Using co-immunoprecipitation, we further demonstrate that human canonical CRB1 interacts with CRB1 and CRB2, but not with CRB3, which lacks an extracellular domain. Next, we explored how missense mutations in the extracellular domain affect CRB1–CRB2 interactions. We observed no or a mild loss of CRB1–CRB2 interaction, when interrogating various CRB1 or CRB2 missense mutants in vitro. Taken together, our results show a stable interaction of human canonical CRB2 and CRB1 in the retina.
The redox-sensitive R-loop of the carbon control protein SbtB contributes to the regulation of the cyanobacterial CCM
2024-04-03

Abstract SbtB is a PII-like protein that regulates the carbon-concentrating mechanism (CCM) in cyanobacteria. SbtB proteins can bind many adenyl nucleotides and possess a characteristic C-terminal redox sensitive loop (R-loop) that forms a disulfide bridge in response to the diurnal state of the cell. SbtBs also possess an ATPase/ADPase activity that is modulated by the redox-state of the R-loop. To investigate the R-loop in the cyanobacterium Synechocystis sp. PCC 6803, site-specific mutants, unable to form the hairpin and permanently in the reduced state, and a R-loop truncation mutant, were characterized under different inorganic carbon (C i ) and light regimes. Growth under diurnal rhythm showed a role of the R-loop as sensor for acclimation to changing light conditions. The redox-state of the R-loop was found to impact the binding of the adenyl-nucleotides to SbtB, its membrane association and thereby the CCM regulation, while these phenotypes disappeared after truncation of the R-loop. Collectively, our data imply that the redox-sensitive R-loop provides an additional regulatory layer to SbtB, linking the CO 2 -related signaling activity of SbtB with the redox state of cells, mainly reporting the actual light conditions. This regulation not only coordinates CCM activity in the diurnal rhythm but also affects the primary carbon metabolism.
Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense
2024-04-03

Understanding the genomic basis of natural variation in plant pest resistance is an important goal in plant science, but it usually requires large and labor-intensive phenotyping experiments. Here, we explored the possibility that non-target reads from plant DNA sequencing can serve as phenotyping proxies for addressing such questions. We used data from a whole-genome and -epigenome sequencing study of 207 natural lines of field pennycress ( Thlaspi arvense ) that were grown in a common environment and spontaneously colonized by aphids, mildew, and other microbes. We found that the numbers of non-target reads assigned to the pest species differed between populations, had significant SNP-based heritability, and were associated with climate of origin and baseline glucosinolate contents. Specifically, pennycress lines from cold and thermally fluctuating habitats, presumably less favorable to aphids, showed higher aphid DNA load, i.e., decreased aphid resistance. Genome-wide association analyses identified genetic variants at known defense genes but also novel genomic regions associated with variation in aphid and mildew DNA load. Moreover, we found several differentially methylated regions associated with pathogen loads, in particular differential methylation at transposons and hypomethylation in the promoter of a gene involved in stomatal closure, likely induced by pathogens. Our study provides first insights into the defense mechanisms of Thlaspi arvense , a rising crop and model species, and demonstrates that non-target whole-genome sequencing reads, usually discarded, can be leveraged to estimate intensities of plant biotic interactions. With rapidly increasing numbers of large sequencing datasets worldwide, this approach should have broad application in fundamental and applied research.
Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense
2024-04-03

Abstract Understanding the genomic basis of natural variation in plant pest resistance is an important goal in plant science, but it usually requires large and labour-intensive phenotyping experiments. Here, we explored the possibility that non-target reads from plant DNA sequencing can serve as phenotyping proxies for addressing such questions. We used data from a whole-genome and -epigenome sequencing study of 207 natural lines of field pennycress (Thlaspi arvense) that were grown in a common environment and spontaneously colonized by aphids, mildew and other microbes. We found that the numbers of non-target reads assigned to the pest species differed between populations, had significant SNP-based heritability, and were associated with climate of origin and baseline glucosinolates content. Specifically, pennycress lines from cold and thermally fluctuating habitats, presumably less favorable to aphids, showed higher aphid DNA load, i.e. decreased aphid resistance. Genome-wide association analyses identified genetic variants at known defense genes but also novel genomic regions associated with variation in aphid and mildew DNA load. Moreover, we found several differentially methylated regions associated with pathogen loads, in particular differential methylation at transposons and hypomethylation in the promoter of a gene involved in stomatal closure, likely induced by pathogens. Our study provides first insights into the defense mechanisms of Thlaspi arvense, a rising crop and model species, and demonstrates that non-target whole genome sequencing reads, usually discarded, can be leveraged to estimate intensities of plant biotic interactions. With rapidly increasing numbers of large sequencing datasets worldwide, this approach should have broad application in fundamental and applied research.
Bioavailable 87 Sr/ 86 Sr variability and Bronze and Iron Ages caprine mobility on the Balearic Islands (Spain)
2024-04-03

This paper presents the most extensive 87Sr/86Sr datasets from Late Prehistory contexts in addition to bioavailable 87Sr/86Sr values for baseline characterization on the Balearic Islands. A total of 149 caprine dental enamel samples from Mallorca, Menorca, and Formentera islands (Spain), and 35 environmental baseline samples covering the main geologies of these islands are presented here. In addition, a combination of strontium and oxygen sequential analysis was performed on seven individuals from two sites that showed some of the most diverse 87Sr/86Sr values to better understand their mobility patterns. The main goal of this research is to provide more information about isotopic variability of bioavailable strontium on the Balearic Islands and livestock management during the Bronze and Iron Ages, thus allowing us to understand how human communities exploited their landscape and interacted with other populations
Decoding region-level visual functions from invasive EEG data
2024-04-03

Abstract Decoding vision is an ambitious task as it aims to transform scalar brain activity into dynamic images with refined shapes, colors and movements. In familiar environments, the brain may trigger activity that resembles specific pattern, thereby facilitating decoding. Can an artificial neural network (ANN) decipher such latent patterns? Here, we explore this question using invasive electroencephalography data from monkeys. By decoding multiregion brain activity, ANN effectively captures individual regions’ functional roles as a consequence of minimizing visual errors. For example, ANN recognizes that regions V4 and LIP are involved in visual color and shape processing while MT predominantly handles visual motion, aligning with regional visual functions evident in the brain. ANN likely reconstructs vision by seizing hidden spike patterns, representing stimuli distinctly in a two-dimensional plane. Furthermore, during the encoding process of transforming visual stimuli into neuronal activity, optimal performance is achieved in regions closely associated with vision processing.
Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery
2024-04-04

Abstract DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO2 emissions low. The code is available at https://nf-co.re/sarek.
Near-Infrared II Photobiomodulation Preconditioning Ameliorates Stroke Injury via Phosphorylation of eNOS
2024-04-04

BACKGROUND: The current management of patients with stroke with intravenous thrombolysis and endovascular thrombectomy is effective only when it is timely performed on an appropriately selected but minor fraction of patients. The development of novel adjunctive therapy is highly desired to reduce morbidity and mortality with stroke. Since endothelial dysfunction is implicated in the pathogenesis of stroke and is featured with suppressed endothelial nitric oxide synthase (eNOS) with concomitant nitric oxide deficiency, restoring endothelial nitric oxide represents a promising approach to treating stroke injury. METHODS: This is a preclinical proof-of-concept study to determine the therapeutic effect of transcranial treatment with a low-power near-infrared laser in a mouse model of ischemic stroke. The laser treatment was performed before the middle cerebral artery occlusion with a filament. To determine the involvement of eNOS phosphorylation, unphosphorylatable eNOS S1176A knock-in mice were used. Each measurement was analyzed by a 2-way ANOVA to assess the effect of the treatment on cerebral blood flow with laser Doppler flowmetry, eNOS phosphorylation by immunoblot analysis, and stroke outcomes by infarct volumes and neurological deficits. RESULTS: Pretreatment with a 1064-nm laser at an irradiance of 50 mW/cm 2 improved cerebral blood flow, eNOS phosphorylation, and stroke outcomes. CONCLUSIONS: Near-infrared II photobiomodulation could offer a noninvasive and low-risk adjunctive therapy for stroke injury. This new modality using a physical parameter merits further consideration to develop innovative therapies to prevent and treat a wide array of cardiovascular diseases.
Western disturbances and climate variability: a review of recent developments
2024-04-04

Abstract. Western disturbances (WDs) are synoptic-scale weather systems embedded within the subtropical westerly jet. Manifesting as upper-level troughs often associated with a lower-tropospheric low over Western India, they share some dynamical features with extratropical cyclones. WDs are most common during the boreal winter (December to March), during which they bring the majority of precipitation – both rain and snow – to the Western Himalaya, as well as to surrounding areas of north India, Pakistan and the Tibetan Plateau. WDs are also associated with weather hazards such as heavy snowfall, hailstorms, fog, cloudbursts, avalanches, frost, and coldwaves. In this paper, we review the recent understanding and development on WDs. Recent studies have collectively made use of novel data, novel analysis techniques, and the increasing availability of high-resolution weather and climate models. This review is separated into six main sections – structure and thermodynamics, precipitation and impacts, teleconnections, modelling experiments, forecasting at a range of scales, and paleoclimate and climate change – each motivated with a brief discussion of the accomplishments and limitations of previous research. A number of step changes in understanding are synthesised. Use of new modelling frameworks and tracking algorithms has significantly improved knowledge of WD structure and variability, and a more frequentist approach can now be taken. Improved observation systems have helped quantification of water security over the Western Himalaya. Convection-permitting models have improved our understanding of how WDs interact with the Himalayas to trigger natural hazards. Improvements in paleoclimate and future climate modelling experiments have helped to explain how WDs and their impacts over the Himalaya respond to large-scale natural and anthropogenic forcings. We end by summarising unresolved questions and outlining key future WD research topics.
Characteristics and outcomes of cerebral venous thrombosis associated with COVID-19
2024-04-04

Introduction: Previous reports and meta-analyses derived from small case series reported a mortality rate of up to 40% in patients with coronavirus disease 2019 associated cerebral venous thrombosis (COVID-CVT). We assessed the clinical characteristics and outcomes in an international cohort of patients with COVID-CVT. Patients and methods: This was a registry study of consecutive COVID-CVT patients diagnosed between March 2020 and March 2023. Data collected by the International Cerebral Venous Thrombosis Consortium from patients with CVT diagnosed between 2017 and 2018 served as a comparison. Outcome analyses were adjusted for age and sex. Results: We included 70 patients with COVID-CVT from 23 hospitals in 15 countries and 206 controls from 14 hospitals in 13 countries. The proportion of women was smaller in the COVID-CVT group (50% vs 68%, p &lt; 0.01). A higher proportion of COVID-CVT patients presented with altered mental state (44% vs 25%, p &lt; 0.01), the median thrombus load was higher in COVID-CVT patients (3 [IQR 2–4] vs 2 [1–3], p &lt; 0.01) and the length of hospital stay was longer compared to controls (11 days [IQR 7–20] vs 8 [4–15], p = 0.02). In-hospital mortality did not differ (5/67 [7%, 95% CI 3–16] vs 7/206 [3%, 2–7], aOR 2.6 [95% CI 0.7–9]), nor did the frequency of functional independence after 6 months (modified Rankin Scale 0–2; 45/58 [78%, 95% CI 65–86] vs 161/185 [87%, 81–91], aOR 0.5 [95% CI 0.2–1.02]). Conclusion: In contrast to previous studies, the in-hospital mortality rate and functional outcomes during follow-up did not differ between COVID-CVT patients and the pre-COVID-19 controls.
Improvement in Visceral Adipose Tissue and LDL Cholesterol by High PUFA Intake: 1-Year Results of the NutriAct Trial
2024-04-04

We assessed the effect of a dietary pattern rich in unsaturated fatty acids (UFA), protein and fibers, without emphasizing energy restriction, on visceral adipose tissue (VAT) and cardiometabolic risk profile. Within the 36-months randomized controlled NutriAct trial, we randomly assigned 502 participants (50–80 years) to an intervention or control group (IG, CG). The dietary pattern of the IG includes high intake of mono-/polyunsaturated fatty acids (MUFA/PUFA 15–20% E/10–15% E), predominantly plant protein (15–25% E) and fiber (≥30 g/day). The CG followed usual care with intake of 30% E fat, 55% E carbohydrates and 15% E protein. Here, we analyzed VAT in a subgroup of 300 participants via MRI at baseline and after 12 months, and performed further metabolic phenotyping. A small but comparable BMI reduction was seen in both groups (mean difference IG vs. CG: −0.216 kg/m2 [−0.477; 0.045], partial η2 = 0.009, p = 0.105). VAT significantly decreased in the IG but remained unchanged in the CG (mean difference IG vs. CG: −0.162 L [−0.314; −0.011], partial η2 = 0.015, p = 0.036). Change in VAT was mediated by an increase in PUFA intake (ß = −0.03, p = 0.005) and induced a decline in LDL cholesterol (ß = 0.11, p = 0.038). The NutriAct dietary pattern, particularly due to high PUFA content, effectively reduces VAT and cardiometabolic risk markers, independent of body weight loss.
No one home? New evidence for MIS 3 occupations in the Western Cape (South Africa) from Mertenhof Rock Shelter
2024-04-04

<title>Abstract</title> Southern Africa features an intensively studied Stone Age sequence, though one with geographical and temporal gaps. The archaeology of Marine Isotope Stage (MIS) 3 remains understudied, particularly between ~ 50 − 25 ka. This period encompasses numerous ecological, demographic and behavioural changes, most notably the passage from Middle Stone Age (MSA) to Later Stone Age (LSA) technologies. In western South Africa, previous research postulated a hiatus in the cultural sequence during the second half of MIS 3, potentially reflecting depopulation due to hyperarid environments. Here we document rare occupations during this period in the Western Cape at Mertenhof Rock Shelter (MRS) by providing new chronometric and technological data. OSL estimates suggest two pulses of low-density occupations at ~ 50 ka and 41 − 37 ka, allowing for a diachronic assessment of technological changes. These sporadic MSA occupations complement the more widespread occurrence of open-air settlements along the Doring River during ~ 50 − 35 ka. At MRS, knappers procured local rock types and produced small flakes and some blades via platform and bipolar reduction but without Nubian methods. The retouched pieces feature splintered pieces and denticulates but mostly lack points. Notable differences to sites in eastern southern Africa underscore ongoing technological regionalization and demographic partitioning during MIS 3. The temporal changes in the sequence show no consistent trajectory towards the ELSA in the region that appears around 25 ka. Lithic and chronometric evidence from MRS supports scenarios of a long persistence of the MSA within MIS 3 in southern Africa and a late emergence of the LSA after 35 ka.