Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression has Distinct Associations with Brain Structure and Function in Major Depressive Disorder

Major depressive disorder (MDD) is associated with structural and functional brain abnormalities. MDD as well as brain anatomy and function are influenced by genetic factors, but the role of gene expression remains unclear. Here, this work investigates how cortical gene expression contributes to structural and functional brain abnormalities in MDD. This work compares the gray matter volume and resting‐state functional measures in a Chinese sample of 848 MDD patients and 749 healthy controls, and these case‐control differences are then associated with cortical variation of gene expression. While whole gene expression is positively associated with structural abnormalities, it is negatively associated with functional abnormalities. This work observes the relationships of expression levels with brain abnormalities for individual genes, and found that transcriptional correlates of brain structure and function show opposite relations with gene dysregulation in postmortem cortical tissue from MDD patients. This work further identifies genes that are positively or negatively related to structural abnormalities as well as functional abnormalities. The MDD‐related genes are enriched for brain tissue, cortical cells, and biological pathways. These findings suggest that distinct genetic mechanisms underlie structural and functional brain abnormalities in MDD, and highlight the importance of cortical gene expression for the development of cortical abnormalities.
Measurement of the beta-nu correlation coefficient a(beta nu) in the beta decay of trapped He-6(+) ions

We have measured the β-ν angular correlation in the β decay of 6He+ ions using a transparent Paul trap. The 6He+ ions, produced at GANIL, were first cooled and bunched before being injected in the LPCTrap setup. The angular correlation was inferred from the time of flight of recoil nuclei detected in coincidence with the β particles. The detection system gives access to the full β decay kinematics, providing means to check the data reliability and to reject a large fraction of background. We find aβν = −0.3335(73)stat(75)syst, in agreement with the standard model prediction for a pure Gamow-Teller transition.
Bio-inspired mechanics of bottom-up designed hierarchical materials: robust and releasable adhesion systems of gecko.

To explore the basic principles of hierarchical materials designed from nanoscale and up, we have been studying the mechanics of robust and releasable adhesion nanostructures of gecko [1]. On the question of robust adhesion, we have introduced a fractal-like hierarchical hair model to show that structural hierarchy allows the work of adhesion to be exponentially enhanced as the level of structural hierarchy is increased. We show that the nanometer length scale plays an essential role in the bottom-up design and, baring fracture of hairs themselves, a hierarchical hair system can be designed from nanoscale and up to achieve flaw tolerant adhesion at any length scales. For releasable adhesion, we show that elastic anisotropy leads to orientation-dependent adhesion strength. Finite element calculations revealed that a strongly anisotropic attachment pad in contact with a rigid substrate exhibits essentially two levels of adhesion strength depending on the direction of pulling.
Extragastric recurrence in patients who underwent surgical resection of stage I gastric cancer: Incidence, risk factors, and value of abdominal computed tomography as a postoperative surveillance method

Extragastric recurrence after radical resection of stage I gastric cancer is very rare. We investigated the incidence of extragastric recurrence and risk factors in patients who underwent surgical resection of stage I gastric cancer and evaluated the value of abdominal CT as a surveillance tool. This retrospective study enrolled 914 patients with stage I gastric cancer who underwent surgical resection at a single tertiary hospital. We investigated extragastric recurrence during the follow-up period, and disease-free survival (DFS) was assessed. Over a median follow-up period of 39 months, the overall incidence of extragastric recurrence was 2.2% (20/914). Risk factors for extragastric recurrence included deep submucosal invasion (SM2-3), muscularis propria invasion, and lymph node metastasis (hazard ratio [HR]=10.37, 28.101, and 6.843; P = .028, .002, and .001, respectively). Based on the number of risk factors, patients were stratified into 3 subgroups: low-risk (pT1aN0, pT1b(SM1)N0, 496/914), moderate-risk (pT1aN1, pT1b(SM1)N1, pT1b(SM2-3)N0, pT2N0, 369/914), and high-risk (pT1b(SM2-3)N1, 49/914). DFS was significantly longer in the low-risk group, followed by the moderate-risk and high-risk groups. We propose that postoperative CT surveillance should be omitted for stage 1A cases involving the mucosa and SM1 because of the extreme rarity of extragastric recurrence.
Effects of the nurse-led program on disabilities improvement in patients with ischemic stroke

To evaluate whether the nurse-led program can improve disabilities in patients with ischemic stroke for more than 6 months. This is a randomized, open-label study. Participants in the usual-care group received the usual care that included verbal stroke-related education and secondary prevention. Participants in the active group received the usual care plus the nurse-led program intervention. The disability was evaluated using National Institutes of Health Stroke Scale (NIHSS). The Mental Health Inventory-5 (MHI-5) was used to assess mental health status (MHS). The median duration since ischemic stroke was 8.4 and 8.6 months, respectively. At baseline, there was no difference in the median NIHSS value and the NIHSS category between these 2 groups. After 6 months’ follow-up, the median NIHSS value was lower in the active group (4.1 vs 6.3). The proportion of patients with NIHSS of 1 to 4 was higher (50.0% vs 28.6%) while the proportion of patients with NIHSS of 5 to 12 (24.1% vs 51.8%) was lower in the active group. After multivariate regression analysis, the nurse-led program was negatively associated with increased NIHSS category (odds ratio of 0.70 and 95% confidence interval of 0.62–0.88). In the group with MHI-5 less than median, the nurse-led program was not associated with NIHSS category. While in the group with MHI-5 greater than median, the nurse-led program was associated decreased NIHSS category, with a significant interaction (P value = .03). In ischemic stroke patients for more than 6 months, the nurse-led program improves disabilities, which might be related to MHS improvement.
Prenatal gyrification pattern affects age at onset in frontotemporal dementia

Abstract The paracingulate sulcus is a tertiary sulcus formed during the third trimester. In healthy individuals paracingulate sulcation is more prevalent in the left hemisphere. The anterior cingulate and paracingulate gyri are focal points of neurodegeneration in behavioral variant frontotemporal dementia (bvFTD). This study aims to determine the prevalence and impact of paracingulate sulcation in bvFTD. Structural magnetic resonance images of individuals with bvFTD (n = 105, mean age 66.9 years), Alzheimer’s disease (n = 92, 73.3), and healthy controls (n = 110, 62.4) were evaluated using standard protocol for hemispheric paracingulate sulcal presence. No difference in left hemisphere paracingulate sulcal frequency was observed between groups; 0.72, 0.79, and 0.70, respectively, in the bvFTD, Alzheimer’s disease, and healthy control groups, (P = 0.3). A significant impact of right (but not left) hemispheric paracingulate sulcation on age at disease onset was identified in bvFTD (mean 60.4 years where absent vs. 63.8 where present [P = 0.04, Cohen’s d = 0.42]). This relationship was not observed in Alzheimer’s disease. These findings demonstrate a relationship between prenatal neuronal development and the expression of a neurodegenerative disease providing a gross morphological example of brain reserve.
Relationship between Calcium Score and Conventional Risk Factors in the Diagnosis of Atherosclerosis

Background: The coronary artery calcium score has been established as a highly specific feature of coronary atherosclerosis. The present study aimed to assess the possible association of coronary artery risk factors involving atherosclerosis with the coronary artery calcification (CAC) scores using coronary computed tomographic angiography (CCTA). Methods: The present cross-sectional study, performed on 252 patients in need of CCTA during April 2019 and September 2019 at Farshchian hospital in Hamadan, Iran. The demographic information and risk factors were acquired from the files of patients. Furthermore, the CACs of patients were calculated and expressed as the Agatston score. Based on the Agatston scale, participants were divided into 4 CAC scores: zero (CAC = 0), mild (CAC = 1-99), moderate (CAC = 100-399), and severe (CAC ≥400). The association between possible coronary artery disease (CAD) risk variables and the CAC score was investigated using multinomial logistic regression. Results: Of 252 participants, approximately 40% of studied patients had a positive CAC score (CAC > 0). CAC significantly shifts toward higher scores in smokers, patients with diabetes, hypertension, and older patients. Mild (CAC = 1-99) and moderate CAC (100-399) were significantly associated with diabetes (odds ratio [OR], 3.26; 95% CI, 1.48-7.17) and (OR, 12; 95% CI, 4.40-32.71) for mild and moderate CAC, respectively. However, the strongest predictor for severe CAC was diabetes (OR, 7.72; 95% CI, 2.10-28.35). Conclusion: Coronary artery calcium scoring is a marker for risk factors associated with atherosclerosis. In this study, more than half of patients in CAC screening had CAC = 0. The strongest predictor of severe CAC>0 was smoking and diabetes. Regarding this association between health condition and CAC, determining the CAC can prevent major coronary heart disease events in these patients.
Filtrage d'un processus partiellement observé et équations différentielles stochastiques rétrogrades réfléchies

Cette these comprend deux parties independantes. La premiere partie etudie un probleme de perturbation singuliere en filtrage non lineaire lorsque le processus est partiellement observe. Nous proposons un filtre approche de dimension finie pour la partie observee. A l'aide de ce filtre nous construisons un filtre approche de dimension infinie pour la partie non-observee. Il verifie cependant une equation de type zakai ou la dimension de la variable spatiale est plus petite que celle de l'equation de zakai verifiee par le filtre exact. La methode utilisee donne l'erreur d'approximation entre les deux filtres. La deuxieme partie etablit un theoreme d'existence et d'unicite pour la solution des equations differentielles stochastiques retrogrades (e. D. S. R. ) reflechies dans un convexe sans hypotheses de regularite sur celui-ci. Des conditions suffisantes sont d'abord donnees pour que la solution d'une e. D. S. R. Au sens classique reste dans un convexe donne. Nous montrons ensuite que s'il existe une solution au probleme reflechi, alors celle-ci est unique et le processus de reflexion est absolument continu. Nous montrons enfin l'existence par une methode de penalisation
The Effect of Neoadjuvant vs Adjuvant Chemotherapy on Final Outcome of Patients with Triple Negative Breast Cancer

Background: Triple negative breast cancer (TNBC) accounts for about 10% to 20% of breast cancers, does not respond to endocrine treatment, and is more aggressive. Two chemotherapy methods suggested include neoadjuvant chemotherapy (NAC), performed before surgery, and adjuvant chemotherapy (AC), performed after surgery. In order to determine whether the choice of chemotherapy method has any impact on patients’ outcome, the present study aimed to compare the overall survival (OS) and disease-free survival (DFS) of TNBC patients with a 10-year follow-up. Methods: The present study aimed to investigate the effect of neoadjuvant versus adjuvant chemotherapy on the final outcome of patients with TNBC. Women with TNBC stages II and III who referred to the Cancer Research Center of Shahid Beheshti University of Medical Sciences during 2000 and 2020 were included (N = 237) and visited or called by phone to obtain their consent and complete their information. The participants were categorized into 2 groups according to the treatment protocol they received; one group received NAC (N = 85) and the other group received AC (N = 188); patients’ age, tumor’s grade and stage, lymphovascular invasion (LVI), DFS, and OS were compared between the 2 treatment types. For the statistical analysis, the statistical software IBM SPSS Statistics for Windows, Version 24.0. (IBM Corp) was used. All tests were 2-sided and P values < 0.050 were considered statistically significant. Results: The frequency of pathologies, LVI, and type of surgery was not different between the groups (p = 0.543, p = 0.352, p = 0.935), while the frequency of age categories and tumor grade was significantly different between the groups (p = 0.003, p = 0.001). Ten-year OS and DFS were not different between the groups (p = 0.771, p = 0.506). The Multivariate Cox analysis results showed clinical stage, pathologic grade, age >70, and LVI as significant predictors of death. Conclusion: These results showed that the choice of chemotherapy method, performed before or after surgery, does not influence the 10-year OS and DFS of TNBC patients.
Parametric study of axial trapping forces on an elliptically symmetric dielectric in the ray optics regime

We present the parametric investigation of the axial trapping forces generated by the interaction of an ellipsoidal dielectric and a focused, randomly polarized Gaussian beam in the geometrical optics regime. We show that particle elongation along the optical axis results to a more unstable axial trap compared to that of a reference sphere due to the more positive axial forces for positive axial displacements. Decreasing the refractive index difference between the particle and the surrounding medium (Δn = 0.09) decreases the magnitude of the axial force for positive particle displacements; and for a narrow range of axial displacements an axial trap can be achieved. Increasing the beam wavelength increases the magnitude of the axial force and for 1060 nm an axial trap can be achieved.
A commutative P^1-spectrum representing motivic cohomology over Dedekind domains

We construct a motivic Eilenberg-MacLane spectrum with a highly structured multiplication over smooth schemes over Dedekind domains which represents Levine's motivic cohomology. The latter is defined via Bloch's cycle complexes. Our method is by gluing p-completed and rational parts along an arithmetic square. Hereby the finite coefficient spectra are obtained by truncated \'etale sheaves (relying on the now proven Bloch-Kato conjecture) and a variant of Geisser's version of syntomic cohomology, and the rational spectra are the ones which represent Beilinson motivic cohomology. As an application the arithmetic motivic cohomology groups can be realized as Ext-groups in a triangulated category of Tate sheaves with integral coefficients. These can be modelled as representations of derived fundamental groups. Our spectrum is compatible with base change giving rise to a formalism of six functors for triangulated categories of motivic sheaves over general base schemes including the localization triangle. Further applications include a generalization of the Hopkins-Morel isomorphism and a structure result for the dual motivic Steenrod algebra in the case where the coefficient characteristic is invertible on the base scheme.
Update, the infinite case

We provide a set of postulates that characterizes Katsuno and Mendelzon’s update operation [3] for a possibly infinite propositional language. In this way we extend their original operator which was only defined for finite languages. After reformulating the update operation as a function on theories, we show that Katsuno and Mendelzon’s original postulates are not sufficient to provide a characterization theorem. A strengthening of postulate (U8) is needed for a representation result. The new definition of update on (possibly infinite) languages puts the two main notions of theory change (update and revision) in the same ground and opens the way to a better comparison of their properties.
Imaging the Hot Molecular Gas at the Centre of the Galaxy

Abstract The AAT’S new IR array camera, IRIS, has been used to image the Galactic Centre in the He I (2.058μm), H+ Br γ(2.166μm) and H2 1-0 S(l) (2.122μm) emission lines. The case is presented for UV-excitation of the molecular gas, as opposed to shocks.
Overview of Core Diagnostics for TEXTOR

Abstract The diagnostic system of TEXTOR comprises about 50 individual diagnostic devices. Since the start of the Trilateral Euregio Cluster collaboration, part of the emphasis in the experimental program has shifted toward the study of physics processes in the plasma core. To aid these studies several new and advanced core diagnostics have been implemented, whereas a number of other core diagnostics have been upgraded to higher resolution, more channels, and better accuracy. In this paper a brief overview is given of the present set of plasma core diagnostics at TEXTOR.
Subarachnoidal hemorrhage related cardiomyopathy: an overview of Tako-Tsubo cardiomyopathy and related cardiac syndromes

ABSTRACT Introduction Subarachnoid hemorrhage (SAH) is caused by a ruptured intracranial aneurysm leading to acute extravasation of blood into the subarachnoid space. SAH has an incidence of 6.3 per 100,000 persons per year in Europe and accounts for 5% of all strokes. SAH occurs at a relatively young age and has poor clinical outcomes and high mortality rates. Cardiac syndromes are regularly seen in patients with acute neurologic disease including SAH. These cardiac complications of SAH are associated with increased morbidity and mortality and present in a large variety and severity. Areas covered The main goal of this review is to describe the SAH-related cardiac syndromes. Secondly, we will provide an overview of the underlying pathophysiology regarding the development of cardiac syndromes. Thirdly, we will describe the impact of cardiac syndromes on patient outcome. Expert opinion Of all neurology patients, SAH patients have the highest risk of developing takotsubo syndrome (TTS), occurring in about 0.8–30% of patients. Both TTS and neurogenic stunned myocardium have many similarities on echocardiographic evaluation. In European Cardiology consensus, SAH is recognized as a primary cause of TTS.
The Angular Gyrus as a Hub for Modulation of Language-related Cortex by Distinct Prefrontal Executive Control Regions

Abstract It has become clear in recent years that reading, while relying on domain-specific language processing regions, also involves regions that implement executive processes more broadly. Such executive control is generally considered to be implemented by prefrontal regions, which exert control via connectivity that allows them to modulate processing in target brain regions. The present study examined whether three previously identified and distinct executive control regions in the pFC [Wang, K. , Banich, M. T. , Reineberg, A. E. , Leopold, D. R. , Willcutt, E. G. , Cutting, L. E. , et al. Left posterior prefrontal regions support domain-general executive processes needed for both reading and math. Journal of Neuropsychology, 14, 467–495, 2020] show similar patterns of functional connectivity (FC) during a reading comprehension task as compared with a symbol identification condition. Our FC results in a sample of adolescents (n = 120) suggest all three regions commonly show associations with activity in “classic” left hemisphere reading areas, including the angular and supramarginal gyri, yet each exhibits differential connectivity as well. In particular, precentral regions show differential FC to parietal portions of the dorsal language stream, the inferior frontal junction shows differential FC to middle temporal regions of the right hemisphere and other regions involved in semantic processing, and portions of the inferior frontal gyrus show differential FC to an extensive set of right hemisphere prefrontal regions. These results suggest that prefrontal control over language-related regions occurs in a coordinated yet discrete manner.
Human cone elongation responses can be explained by photoactivated cone opsin and membrane swelling and osmotic response to phosphate produced by RGS9-catalyzed GTPase

Significance Optical coherence tomography has established that human cone photoreceptor outer segments elongate in response to stimuli bleaching large fractions of their visual pigment. Elongation responses are completely described over their 200-fold bleaching range as the sum of two exponentially rising components differing 13-fold in time constants and 4-fold in light sensitivity. Bleaching measurements of individual cones with adaptive optics scanning laser ophthalmoscopy (SLO) suggest that component 2 arises from cone opsin and disk membrane swelling triggered by photoactivation. Application of a model of phototransduction suggests that component 1 corresponds to free phosphate generated by regulator of G-protein signaling 9 (RGS9)-catalyzed hydrolysis of guanosine triphosphate (GTP) in the α-subunit of G protein complexed with phosphodiesterase.
MERRIN: MEtabolic regulation rule INference from time series data.

MOTIVATION Many techniques have been developed to infer Boolean regulations from a prior knowledge network (PKN) and experimental data. Existing methods are able to reverse-engineer Boolean regulations for transcriptional and signaling networks, but they fail to infer regulations that control metabolic networks. RESULTS We present a novel approach to infer Boolean rules for metabolic regulation from time-series data and a PKN. Our method is based on a combination of answer set programming and linear programming. By solving both combinatorial and linear arithmetic constraints, we generate candidate Boolean regulations that can reproduce the given data when coupled to the metabolic network. We evaluate our approach on a core regulated metabolic network and show how the quality of the predictions depends on the available kinetic, fluxomics or transcriptomics time-series data. AVAILABILITY AND IMPLEMENTATION Software available at https://github.com/bioasp/merrin. SUPPLEMENTARY INFORMATION Supplementary data are available at https://doi.org/10.5281/zenodo.6670164.
FPM Simulations of a 3D Impinging Jet on a Flat Plate Comparison with CFD and Experimental Results

The present paper reports the development of Finite Particle Method (FPM) in the framework of 3D impinging jet simulations. The FPM kernel has been proposed recently in the literature to improve the consistency of standard SPH. Moreover, a new particle shifting method is proposed to mitigate the particle clustering issue. The influence of particle spacing, maximum CFL number and different particle shifting methods are investigated in the case of a water jet impinging perpendicularly on a flat plate. The results are compared to available measurements and grid-based CFD simulations.