julilili42/papers huggingface dataset:
Quantitative Contribution of Oxygen Vacancy Defects to Arsenate Immobilization on Hematite
2023-08-10

Hematite is a common iron oxide in natural environments, which has been observed to influence the transport and fate of arsenate by its association with hematite. Although oxygen vacancies were demonstrated to exist in hematite, their contributions to the arsenate immobilization have not been quantified. In this study, hematite samples with tunable oxygen vacancy defect (OVD) concentrations were synthesized by treating defect-free hematite using different NaBH<sub>4</sub> solutions. The vacancy defects were characterized by positron annihilation lifetime spectroscopy, Doppler broadening of annihilation radiation, extended X-ray absorption fine structure (EXAFS), thermogravimetric mass spectrometry (TG-MS), electron paramagnetic resonance (EPR), and X-ray photoelectron spectroscopy (XPS). The results revealed that oxygen vacancy was the primary defect type existing on the hematite surface. TG-MS combined with EPR analysis allowed quantification of OVD concentrations in hematite. Batch experiments revealed that OVDs had a positive effect on arsenate adsorption, which could be quantitatively described by a linear relationship between the OVD concentration (<i>C</i><sub>def</sub>, mmol m<sup>-2</sup>) and the enhanced arsenate adsorption amount caused by defects (Δ<i>Q</i><sub>m</sub>, μmol m<sup>-2</sup>) (Δ<i>Q</i><sub>m</sub> = 20.94 <i>C</i><sub>def</sub>, <i>R</i><sup>2</sup> = 0.9813). NH<sub>3</sub>-diffuse reflectance infrared Fourier transform (NH<sub>3</sub>-DRIFT) analysis and density functional theory (DFT) calculations demonstrated that OVDs in hematite were beneficial to the improvement in adsorption strength of surface-active sites, thus considerably promoting the immobilization of arsenate.
The clinical and molecular taxonomy of t(14;18)-negative follicular lymphomas
2023-08-10

Abstract Follicular lymphoma (FL) is a neoplasm derived from germinal center B cells, composed of centrocytes and centroblasts, with at least a focal follicular growth pattern. The t(14;18) translocation together with epigenetic deregulation through recurrent genetic alterations are now recognized as the hallmark of FL. Nevertheless, FL is a heterogeneous disease, clinically, morphologically, and biologically. The existence of FL lacking the t(14;18) chromosomal alteration highlights the complex pathogenesis of FL, and indicates that there are alternative pathogenetic mechanisms that can induce a neoplasm with follicular center B-cell phenotype. Based on their clinical presentation, t(14;18)-negative FLs can be divided into 3 broad groups: nodal presentation, extranodal presentation, and those affecting predominantly children and young adults. Recent studies have shed some light into the genetic alterations of t(14;18)-negative FL. Within the group of t(14;18)-negative FL with nodal presentation, cases with STAT6 mutations are increasingly recognized as a distinctive molecular subgroup, often cooccurring with CREBBP and/or TNFRSF14 mutations. FL with BCL6 rearrangement shows clinicopathological similarities to its t(14;18)-positive counterpart. In contrast, t(14;18)-negative FL in extranodal sites is characterized mainly by TNFRSF14 mutations in the absence of chromatin modifying gene mutations. FL in children have a unique molecular landscape when compared with those in adults. Pediatric-type FL (PTFL) is characterized by MAP2K1, TNFRSF14, and/or IRF8 mutations, whereas large B-cell lymphoma with IRF4 rearrangement is now recognized as a distinct entity, different from PTFL. Ultimately, a better understanding of FL biology and heterogeneity should help to understand the clinical differences and help guide patient management and treatment decisions.
The impact of distractor relevance on the strength and timing of cognitive control: Evidence from delta plots and diffusion model analyses.
2023-08-10

In the present study, we examined how the relevance of potentially distracting information modulates the interplay of target and distractor processing in conflict tasks. Specifically, we manipulated the degree to which distracting information is relevant for performing the overall task by varying the proportion of trials in which a response to the distractor(s) (Experiments 1a and 1b: location in a Simon task; Experiment 2: flankers in an Eriksen flanker task) instead of to the target was required. Across all experiments, the congruency effect on mean RT was larger with the increasing relevance of the distractor(s). Critically, the slopes of the delta plot were more strongly increasing when the distractors were potentially relevant (as opposed to completely irrelevant), suggesting that cognitive control affects the timing of suppressing distractor-based activation. In addition, delta plot and diffusion model analyses revealed that the strength of suppressing distractor processing and the efficiency of target processing were enhanced when the distractors were less relevant. Overall, the present study dissociated multiple and time-dependent adjustments of control processes (i.e., target processing enhancement plus timing and strength of distractor suppression) in environments that encourage either a more stable or more flexible processing mode. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
Novel insights into the pathogenesis of follicular lymphoma by molecular profiling of localized and systemic disease forms
2023-08-10

Abstract Knowledge on the pathogenesis of FL is mainly based on data derived from advanced/systemic stages of FL (sFL) and only small cohorts of localized FL (lFL) have been characterized intensively so far. Comprehensive analysis with profiling of somatic copy number alterations (SCNA) and whole exome sequencing (WES) was performed in 147 lFL and 122 sFL. Putative targets were analyzed for gene and protein expression. Overall, lFL and sFL, as well as BCL2 translocation-positive ( BCL2 +) and –negative ( BCL2 −) FL showed overlapping features in SCNA and mutational profiles. Significant differences between lFL and sFL, however, were detected for SCNA frequencies, e.g., in 18q-gains (14% lFL vs. 36% sFL; p = 0.0003). Although rare in lFL, gains in 18q21 were associated with inferior progression-free survival (PFS). The mutational landscape of lFL and sFL included typical genetic lesions. However, ARID1A mutations were significantly more often detected in sFL (29%) compared to lFL (6%, p = 0.0001). In BCL2 + FL mutations in KMT2D , BCL2 , ABL2 , IGLL5 and ARID1A were enriched, while STAT6 mutations more frequently occurred in BCL2 - FL. Although the landscape of lFL and sFL showed overlapping features, molecular profiling revealed novel insights and identified gains in 18q21 as prognostic marker in lFL.
Adrenal Crisis – Definition, Prevention and Treatment: Results from a Delphi Survey
2023-08-10

Abstract Based on recent data, a total number of about 29 000 patients with adrenal insufficiency can be calculated for Germany, and about 1500 fatalities due to adrenal crises have to be expected within the next decade. Management of adrenal crises is still unsatisfactory. The objectives of this study were to establish consensus for diagnostic criteria, prevention strategies, and treatment recommendations for adrenal crises. The study was conducted from January 2022 to April 2023, using Delphi technique. Four rounds of questionnaires were sent to 45 experts, selected by a coordinating group on behalf of the adrenal section of the German Society of Endocrinology. The survey was implemented online using the REDCap web application. Responses were captured anonymously. During the Delphi process the expert panel developed diagnostic criteria to identify patients likely to have an adrenal crisis. Education about adrenal insufficiency among patients as well as non-endocrine medical personnel were regarded as highly important. It was suggested that recommendations for the management of adrenal insufficiency have to be simplified and made widely available. This study provides pragmatic strategies to identify and treat patients prone to adrenal crisis, thereby highlighting the need for an improved management of patients with adrenal insufficiency.
Freeze-dried nanocrystal dispersion of novel deuterated pyrazoloquinolinone ligand (DK-I-56-1): Process parameters and lyoprotectant selection through the stability study
2023-08-10

Recently, nanocrystal dispersions have been considered as a promising formulation strategy to improve the bioavailability of the deuterated pyrazoloquinolinone ligand DK-I-56-1 (7‐methoxy-2-(4‐methoxy-d3-phenyl)-2,5-dihydro-3H-pyrazolo[4,3-c]quinolin-3-one). In the current study, the freeze-drying process (formulation and process parameters) was investigated to improve the storage stability of the previously developed formulation. Different combinations of lyoprotectant (sucrose or trehalose) and bulking agent (mannitol) were varied while formulations were freeze-dried under two conditions (primary drying at -10 or -45 °C). The obtained lyophilizates were characterized in terms of particle size, solid state properties and morphology, while the interactions within the samples were analyzed by Fourier transform infrared spectroscopy. In the preliminary study, three formulations were selected based on the high redispersibility index values (around 95%). The temperature of primary drying had no significant effect on particle size, but stability during storage was impaired for samples dried at -10 °C. Samples dried at lower temperature were more homogeneous and remained stable for three months. It was found that the optimal ratio of sucrose or trehalose to mannitol was 3:2 at a total concentration of 10% to achieve the best stability (particle size < 1.0 μm, polydispersity index < 0.250). The amorphous state of lyoprotectants probably provided a high degree of interaction with nanocrystals, while the crystalline mannitol provided an elegant cake structure. Sucrose was superior to trehalose in maintaining particle size during freeze-drying, while trehalose was more effective in keeping particle size within limits during storage. In conclusion, results demonstrated that the appropriate combination of sucrose/trehalose and mannitol together with the appropriate selection of lyophilization process parameters could yield nanocrystals with satisfactory stability.
The Gods of the Sea
2023-08-10

Japan is often imagined as a nation with a long history of whaling. In this innovative new study, Fynn Holm argues that for centuries some regions in early modern Japan did not engage in whaling. In fact, they were actively opposed to it, even resorting to violence when whales were killed. Resistance against whaling was widespread especially in the Northeast among the Japanese fishermen who worshiped whales as the incarnation of Ebisu, the god of the sea. Holm argues that human interactions with whales were much more diverse than the basic hunter-prey relationship, as cetaceans played a pivotal role in proto-industrial fisheries. The advent of industrial whaling in the early twentieth century, however, destroyed this centuries-long equilibrium between humans and whales. In its place, communities in Northeast Japan invented a new whaling tradition, which has almost completely eclipsed older forms of human-whale interactions. This title is also available as Open Access.
Comparative analysis of the complete mitogenome of Geoffroea decorticans: a native tree surviving in the Atacama Desert
2023-08-10

Chañar ( Geoffroea decorticans (Gill., ex Hook. &amp;amp; Arn.) Burkart) has been highly significant for indigenous people in the Atacama Desert for over 3,000 years. Through evolutionary processes, the G. decorticans mitogenome likely underwent changes facilitating its adaptation to the extreme conditions of the Atacama Desert. Here, we compare the mitochondrial genome of G. decorticans with those of other Papilionoideae family species. The complete mitogenome of G. decorticans was sequenced and assembled, making it the first in the genus Geoffroea . The mitogenome contained 383,963 base pairs, consisting of 33 protein coding genes, 21 transfer RNA genes, and 3 ribosomal RNA genes. The Chañar mitogenome is relatively compact, and has two intact genes ( sdh4 and nad1 ) which were not observed in most other species. Additionally, Chañar possessed the highest amount of mitochondrial DNA of plastid origin among angiosperm species. The phylogenetic analysis of the mitogenomes of Chañar and 12 other taxa displayed a high level of consistency in taxonomic classification, when compared to those of the plastid genome. Atp8 was subjected to positive selection, while the ccmFc and rps1 were subjected to neutral selection. This study provides valuable information regarding its ability to survive the extreme environmental conditions of the Atacama Desert.
The Interplay of Task Characteristics, Linguistic Complexity, and Language Proficiency in High‐Stakes English as a Foreign Language Writing
2023-08-10

Abstract The linguistic characteristics of text productions depend on various factors, including individual language proficiency as well as the tasks used to elicit the production. To date, little attention has been paid to whether some writing tasks are more suitable than others to represent and differentiate students' proficiency levels. This issue is especially relevant in the context of high‐stakes language examinations. In this study, we investigated task effects in English as a foreign language (EFL) Abitur examinations, the high‐stakes test qualifying for higher education admission in Germany. Based on texts produced by 362 students, we examined (a) if and how student writings differ in their linguistic complexity and (b) if the EFL Abitur tasks are equally suited to differentiate the students' proficiency levels. We used a broad operationalization of linguistic complexity, including measures from various linguistic domains in the computational analysis of the texts. The results of our mixed‐effects models show that student texts differ in their linguistic complexity primarily by the functional needs of the task types employed ( summary , analysis , and argumentation ). Furthermore, writing tasks that demand high independence in language performance are best suited to differentiate between proficiency levels, which becomes especially evident in vocabulary choice and usage.
Strain induced reactivity of cyclic iminoboranes: The (2 + 2) cycloaddition of a 1-H-1,3,2-diazaborepine with ethene
2023-08-10

Iminoboranes have gathered immense attention due to their reactivity and potential applications as isoelectronic and isosteric alkynes. While cyclic alkynes are well investigated and useful reagents, cyclic iminoboranes are underexplored and their existence was inferred only via trapping experiments. We report the first direct spectroscopic evidence of a cyclic seven-membered iminoborane, 1-(tert-butyldimethylsilyl)-1-H-1,3,2-diazaborepine 2, under cryogenic matrix isolation conditions. The amino-iminoborane 2 was photochemically generated in solid argon at 4 K from 1-(tert-butyldimethylsilyl)-2-azido-1,2-dihydro-1,2-azaborine (3) and was characterized using FT-IR, UV-Vis spectroscopy, and computational chemistry. The characteristic BN stretching vibration (1751 cm-1) is shifted by about 240 cm-1 compared to linear amino-iminoboranes indicating a significant weakening of the bond. The Lewis acidity value determined computationally (LAB = 9.1 ± 2.6) is similar to that of boron trichloride, and twelve orders of magnitude lower than that of 1,2-azaborinine (BN-aryne, LAB = 21.5 ± 2.6), a six-membered cyclic iminoborane. In contrast to the latter, the reduced ring strain of 2 precludes nitrogen fixation, but it unexpectedly allows facile (2 + 2) cycloaddition reaction with C2H4 under matrix isolation conditions at 30 K. The reaction of 2 with ethene provides the first example of a (2 + 2) cycloaddition reaction of an iminoborane.
Strain-Release Promoted Thermal [2 + 2] Cycloaddition and Photochemical [2 + 2] Cycloreversion of a Tetraorganylaminoborane
2023-08-10

Tetraorganyl aminoboranes are typically monomeric species, while their hydrides or halides often are dimers or higher oligomers. Aminoboranes composed of 9-borafluorene and epiminoacenes (9,10-dihydro-9,10-anthracene, 1, and 1,4-dihydro-1,4-naphthalene, 2) are reported to spontaneously dimerize at room temperature according to NMR spectroscopy and X-ray crystallography. The reason is elucidated to be associated with the strain of the CNC angle that favors trigonal pyramidal coordination over trigonal planar coordination at nitrogen. As the consequence, the distortion energy of the transition state is low, resulting in a reduced barrier for dimerization of 1 and 2. The dimer of 1 undergoes photoinduced cleavage into monomers.
Recent advances in non-small cell lung cancer targeted therapy; an update review
2023-08-11

Abstract Lung cancer continues to be the leading cause of cancer-related death worldwide. In the last decade, significant advancements in the diagnosis and treatment of lung cancer, particularly NSCLC, have been achieved with the help of molecular translational research. Among the hopeful breakthroughs in therapeutic approaches, advances in targeted therapy have brought the most successful outcomes in NSCLC treatment. In targeted therapy, antagonists target the specific genes, proteins, or the microenvironment of tumors supporting cancer growth and survival. Indeed, cancer can be managed by blocking the target genes related to tumor cell progression without causing noticeable damage to normal cells. Currently, efforts have been focused on improving the targeted therapy aspects regarding the encouraging outcomes in cancer treatment and the quality of life of patients. Treatment with targeted therapy for NSCLC is changing rapidly due to the pace of scientific research. Accordingly, this updated study aimed to discuss the tumor target antigens comprehensively and targeted therapy-related agents in NSCLC. The current study also summarized the available clinical trial studies for NSCLC patients.
Biophysical analysis reveals autophosphorylation as an important negative regulator of LRRK2 dimerization
2023-08-11

Abstract Leucine-rich repeat kinase 2 (LRRK2) is a large, multi-domain protein which is associated with Parkinson’s disease. Although high-resolution structures of LRRK2 are available, little is known about the complex dynamics behind the inter-domain regulation of LRRK2 and its perturbation by pathogenic variants. Previous studies have demonstrated that LRRK2 goes through an oligomerization cycle at the membrane, however it remains unclear in which form it exerts its kinase activity. Moreover, the LRRK2 monomer-dimer equilibrium and associated functional implications at a molecular level also need further investigation. In the present work, we used a multi-faceted approach to better understand LRRK2 oligomerization and suggest a functional model of how LRRK2 interacts with its substrates. To this end, we combined nano differential scanning calorimetry and mass photometry with molecular modelling. The thermal analysis resulted in a multistep denaturation profile, elucidating novel insights into the composite structural organization of the multi-domain protein LRRK2. Furthermore, LRRK2 shows a remarkable thermal stability, confirming its oligomeric nature. By using mass photometry, we could observe a monomer-dimer equilibrium which is altered by R1441G, a pathogenic variant within the Roc-COR interface. Most importantly, we could demonstrate that autophosphorylation induces LRRK2 monomerization, indicating a novel intramolecular feedback mechanism. Finally, we investigated the interaction of LRRK2 with its substrate, RAB10 by integrative computational modelling. The resulting models suggest that the monomeric form of LRRK2 is the favored protein conformation for the interaction with its substrate, leading to an increasing interest in the monomer-dimer equilibrium as a possible intervention point for the pathology.
Dietary carbohydrate quality index (CQI), cardio-metabolic risk factors and insulin resistance among adults with obesity
2023-08-11

Abstract Background Metabolic syndrome (MetS), as a cluster of cardiometabolic risk factors, is a global public health concern due to its increasing prevalence. Considering the previous evidence of the association between carbohydrate quality and cardiometabolic risk factors, our study was aimed to evaluate any possible association between carbohydrate quality index (CQI) and cardiometabolic risk factors among obese adults. Methods In this cross-sectional study, 336 apparently healthy individuals with obesity were participated. Dietary intake was assessed by a semi-quantitative Food Frequency Questionnaire (FFQ), including 168 food items validated for the Iranian population. CQI was calculated with three components of solid carbohydrates to total carbohydrates ratio, dietary fiber intake, and dietary glycemic index (GI). Body composition was determined by bioelectrical impedance analysis (BIA). Blood pressure was measured by sphygmomanometer and enzymatic methods were used to evaluate serum lipid, glucose, and insulin concentrations. Results Subjects in the third quartile of CQI had significantly lower systolic blood pressure (SBP) (P = 0.03) and diastolic blood pressure (DBP) (P = 0.01). Participants in the higher quartiles of CQI had more intake of energy, carbohydrates, fat, saturated fatty acid (SFA), and mono-saturated fatty acid (MUFA) (P &lt; 0.05). Moreover, the homeostasis model assessment of insulin resistance (HOMA-IR) was decreased in the second quartile of CQI [odds ratio (OR) = 0.146, P = 0.01) after adjustment for age, body mass index (BMI), sex, physical activity, socioeconomic status (SES) and energy intake. Conclusion According to our findings, a higher quality of dietary carbohydrates, determined by CQI, could be associated with a lower risk of hypertension.
Short oligomers rather than rings of human RAD52 promote single-strand annealing
2023-08-11

ABSTRACT Genome maintenance and stability rely on the repair of DNA double-strand breaks. The break repair can be mediated by the single-strand annealing protein RAD52. RAD52 forms rings that are thought to promote annealing. However, RAD52’s annealing activity decreases with increasing concentrations that favor ring formation. Thus, which oligomeric form and how RAD52 anneals DNA strands and detects sequence homology is unclear. We combine mass photometry with biochemical assays to quantify oligomeric states of human RAD52 with and without DNA and put forward an alternative mechanism illustrating the critical role of short oligomers for single-stranded DNA annealing. We found that while truncated RAD52 formed undecameric rings at nanomolar concentrations, full-length RAD52 was mostly monomeric at lower nanomolar, physiological concentrations. At higher concentrations, it formed rings with a variable stoichiometry from heptamers to tridecamers. At low concentrations, with hardly any rings present, RAD52 already promoted single-strand annealing. Rings and short oligomers could bind at least two single DNA strands, but if complementary strands were both bound to rings annealing was inhibited. Our findings suggest that single-strand annealing and homology detection is mediated by short oligomers of RAD52 instead of rings.