julilili42/papers huggingface dataset:
Halogen Bonding on Water─A Drop in the Ocean?
2024-09-18

Halogen bonding is a valuable interaction in drug design, offering an unconventional way to influence affinity and selectivity by leveraging the halogen atoms' ability to form directional bonds. The present study evaluates halogen-water interactions within protein binding sites, demonstrating that targeting a water molecule via halogen bonding can in specific cases contribute beneficially to ligand binding. In solving and examining the crystal structure of 2-cyclopentyl-7-iodo-1<i>H</i>-indole-3-carbonitrile bound to DYRK1a kinase, we identified a notable iodine-water interaction, where water accepts a halogen bond with good geometric and energetic features. This starting point triggered further investigations into the prevalence of such interactions across various halogen-bearing ligands (chlorine, bromine, iodine) in the PDB. Using QM calculations (MP2/TZVPP), we highlight the versatility and potential benefits of such halogen-water interactions, particularly when the water molecule is a stable part of the binding site's structured environment. While the interaction energies with water are lower compared to other typical halogen bond acceptors, we deem this different binding strength essential for reducing desolvation costs. We suggest that "interstitial" water molecules, as stable parts of the binding site engaging in multiple strong interactions, could be prime targets for halogen bonding. Further systematic studies, combining high-resolution crystal structures and quantum chemistry, are required to scrutinize whether halogen bonding on water is more than a "drop in the ocean".
Emergence of subharmonics in a microwave driven dissipative Rydberg gas
2024-09-18

Quantum many-body systems near phase transitions respond collectively to externally applied perturbations. We explore this phenomenon in a laser-driven dissipative Rydberg gas that is tuned to a bistable regime. Here two metastable phases coexist, which feature a low and high density of Rydberg atoms, respectively. The ensuing collective dynamics, which we monitor , is characterized by stochastic collective jumps between these two macroscopically distinct many-body phases. We show that the statistics of these jumps can be controlled using a dual-tone microwave field. In particular, we find that the distribution of jump times develops peaks corresponding to subharmonics of the relative microwave detuning. Our study demonstrates the control of collective statistical properties of dissipative quantum many-body systems without the necessity of fine-tuning or of ultracold temperatures. Such robust many-body phenomena may find technological applications in sensing. Published by the American Physical Society 2024
The Rectangular Niobium Oxyiodide Cluster Nb4OI10 – A Narrow Band‐Gap Semiconductor
2024-09-18

Abstract A metal‐rich niobium oxyiodide was prepared by soft reduction of NbI 4 . The structure of the new compound Nb 4 OI 10 was determined by single‐crystal X‐ray diffraction and contains a rectangular Nb 4 (μ 4 ‐O) cluster that is interconnected into layers by iodide ligands. The local structure of the Nb 4 OI 10 cluster bears a close relationship to a defect Nb 6 I 11 structure. The two‐dimensional van der Waals material Nb 4 OI 8 I 4/2 ] is a small band‐gap semiconductor (&lt;1 eV), as analysed by electrical conductivity measurements, photoresponse, experimental band gap determination, and band structure calculation.
Prawitz's completeness conjecture: A reassessment
2024-09-18

Abstract In 1973, Dag Prawitz conjectured that the calculus of intuitionistic logic is complete with respect to his notion of validity of arguments. On the background of the recent disproof of this conjecture by Piecha, de Campos Sanz and Schroeder‐Heister, we discuss possible strategies of saving Prawitz's intentions. We argue that Prawitz's original semantics, which is based on the principal frame of all atomic systems, should be replaced with a general semantics, which also takes into account restricted frames of atomic systems. We discard the option of not considering extensions of atomic systems, but acknowledge the need to incorporate definitional atomic bases in the semantic framework. It turns out that ideas and results by Westerståhl on the Carnap categoricity of intuitionistic logic can be applied to Prawitz semantics. This implies that Prawitz semantics has a status of its own as a genuine, though incomplete, semantics of intuitionstic logic. An interesting side result is the fact that every formula satisfiable in general semantics is satisfiable in an axioms‐only frame (a frame whose atomic systems do not contain proper rules). We draw a parallel between this seemingly paradoxical result and Skolem's paradox in first‐order model theory.
SWIEET—a salt-free alternative to QuEChERS
2024-09-18

Abstract The efficient extraction of various analytes from a wide spectrum of matrices with organic solvents is still a great challenge in analytical chemistry. Especially polar and charged compounds are hard to extract in combination with neutral analytes of intermediate to low polarity. The QuEChERS method is often chosen and has been adapted not only to the analysis of food samples, but also to environmental matrices (soil, wastewater) or biota. In this study, we overcome major drawbacks of QuEChERS such as low recoveries of charged analytes and impairment of downstream analysis by high salt loads. The new extraction method, applicable to liquid and solid samples, is called SWIEET (sugar water isopropanol ethyl nitrile extraction technique). Phase separation of the otherwise miscible extraction solvents water and acetonitrile is achieved by sugaring-out instead of salting-out. Extraction efficiencies were greatly improved by adding isopropanol to the acetonitrile phase. The concentrations of the additives glucose and isopropanol, as well as temperature, were optimized by a design of experiment. Further improvement was achieved through electro- or double-extractions. For all sample types tested (surface water, wastewater treatment plant effluent, tomato, soil, and oats), recoveries and precision were higher with SWIEET than with the established QuEChERS method. From wastewater treatment plant effluent, 75% recovery on average were achieved with our SWIEET method compared to 37% with QuEChERS for a model analyte mixture with polarities of logD pH7 = − 5.7 − 3.5. Higher recoveries and lower standard deviations compared to QuEChERS were achieved especially for polar and charged analytes such as metformin. Handling proved to be easy, since there was no additional solid phase and no tedious weighing of salts. Graphical Abstract
Thinking clearly about time-invariant confounders in cross-lagged panel models: A guide for choosing a statistical model from a causal inference perspective.
2024-09-19

Many statistical models have been proposed to examine reciprocal cross-lagged causal effects from panel data. The present article aims to clarify how these various statistical models control for unmeasured time-invariant confounders, helping researchers understand the differences in the statistical models from a causal inference perspective. Assuming that the true data generation model (i.e., causal model) has time-invariant confounders that were not measured, we compared different statistical models (e.g., dynamic panel model and random-intercept cross-lagged panel model) in terms of the conditions under which they can provide a relatively accurate estimate of the target causal estimand. Based on the comparisons and realistic plausibility of these conditions, we made some practical suggestions for researchers to select a statistical model when they are interested in causal inference. (PsycInfo Database Record (c) 2025 APA, all rights reserved).
Risk Stratification in Nonischemic Dilated Cardiomyopathy Using CMR Imaging
2024-09-19

Importance Accurate risk stratification of nonischemic dilated cardiomyopathy (NIDCM) remains challenging. Objective To evaluate the association of cardiac magnetic resonance (CMR) imaging–derived measurements with clinical outcomes in NIDCM. Data Sources MEDLINE, Embase, Cochrane Library, and Web of Science Core Collection databases were systematically searched for articles from January 2005 to April 2023. Study Selection Prospective and retrospective nonrandomized diagnostic studies reporting on the association between CMR imaging–derived measurements and adverse clinical outcomes in NIDCM were deemed eligible. Data Extraction and Synthesis Prespecified items related to patient population, CMR imaging measurements, and clinical outcomes were extracted at the study level by 2 independent reviewers. Random-effects models were fitted using restricted maximum likelihood estimation and the method of Hartung, Knapp, Sidik, and Jonkman. Main Outcomes and Measures All-cause mortality, cardiovascular mortality, arrhythmic events, heart failure events, and major adverse cardiac events (MACE). Results A total of 103 studies including 29 687 patients with NIDCM were analyzed. Late gadolinium enhancement (LGE) presence and extent (per 1%) were associated with higher all-cause mortality (hazard ratio [HR], 1.81 [95% CI, 1.60-2.04]; P &amp;amp;lt; .001 and HR, 1.07 [95% CI, 1.02-1.12]; P = .02, respectively), cardiovascular mortality (HR, 2.43 [95% CI, 2.13-2.78]; P &amp;amp;lt; .001 and HR, 1.15 [95% CI, 1.07-1.24]; P = .01), arrhythmic events (HR, 2.69 [95% CI, 2.20-3.30]; P &amp;amp;lt; .001 and HR, 1.07 [95% CI, 1.03-1.12]; P = .004) and heart failure events (HR, 1.98 [95% CI, 1.73-2.27]; P &amp;amp;lt; .001 and HR, 1.06 [95% CI, 1.01-1.10]; P = .02). Left ventricular ejection fraction (LVEF) (per 1%) was not associated with all-cause mortality (HR, 0.99 [95% CI, 0.97-1.02]; P = .47), cardiovascular mortality (HR, 0.97 [95% CI, 0.94-1.00]; P = .05), or arrhythmic outcomes (HR, 0.99 [95% CI, 0.97-1.01]; P = .34). Lower risks for heart failure events (HR, 0.97 [95% CI, 0.95-0.98]; P = .002) and MACE (HR, 0.98 [95% CI, 0.96-0.99]; P &amp;amp;lt; .001) were observed with higher LVEF. Higher native T1 relaxation times (per 10 ms) were associated with arrhythmic events (HR, 1.07 [95% CI, 1.01-1.14]; P = .04) and MACE (HR, 1.06 [95% CI, 1.01-1.11]; P = .03). Global longitudinal strain (GLS) (per 1%) was not associated with heart failure events (HR, 1.06 [95% CI, 0.95-1.18]; P = .15) or MACE (HR, 1.03 [95% CI, 0.94-1.14]; P = .43). Limited data precluded definitive analysis for native T1 relaxation times, GLS, and extracellular volume fraction (ECV) with respect to mortality outcomes. Conclusion The presence and extent of LGE were associated with various adverse clinical outcomes, whereas LVEF was not significantly associated with mortality and arrhythmic end points in NIDCM. Risk stratification using native T1 relaxation times, extracellular volume fraction, and global longitudinal strain requires further evaluation.
Differential analgesic effects of high-frequency or accelerated intermittent theta burst stimulation of M1 on experimental tonic pain: Correlations with cortical activity changes assessed by TMS-EEG
2024-09-19

Accelerated intermittent theta burst stimulation (AiTBS) has attracted much attention in the past few years as a new form of brain stimulation paradigm. However, it is unclear the relative efficacy of AiTBS on cortical excitability compared to conventional high-frequency rTMS. Using concurrent TMS and electroencephalogram (TMS-EEG), this study systematically compared the efficacy on cortical excitability and a typical clinical application (i.e. pain), between AiTBS with different intersession interval (ISIs) and 10-Hz rTMS. Participants received 10-Hz rTMS, AiTBS-15 (3 iTBS sessions with a 15-min ISI), AiTBS-50 (3 iTBS sessions with a 50-min ISI), or Sham stimulation over the primary motor cortex on four separate days. All four protocols included a total of 1800 pulses but with different session durations (10-Hz rTMS ​= ​18, AiTBS-15 ​= ​40, and AiTBS-50 ​= ​110 ​min). AiTBS-50 and 10-Hz rTMS were more effective in pain reduction compared to AiTBS-15. Using single-pulse TMS-induced oscillation, our data revealed low gamma oscillation as a shared cortical excitability change across all three active rTMS protocols but demonstrated completely opposite directions. Changes in low gamma oscillation were further associated with changes in pain perception across the three active conditions. In contrast, a distinct pattern of TMS-evoked potentials (TEPs) was revealed, with 10-Hz rTMS decreasing inhibitory N100 amplitude and AiTBS-15 reducing excitatory P60 amplitude. These changes in TEPs were also covarying with low gamma power changes. Sham stimulation indicated no significant effect on either cortical excitability or pain perception. These results are relevant only for provoked experimental pain, without being predictive for chronic pain, and revealed a change in low gamma oscillation, particularly around the very particular frequency of 40 ​Hz, shared between AiTBS and high-frequency rTMS. Conversely, cortical excitability (balance between excitation and inhibition) assessed by TEP recording was modulated differently by AiTBS and high-frequency rTMS paradigms.
Attention to food stimuli in binge eating disorder: Electrophysiological evidence
2024-09-19

Attentional biases towards food play an important role in the pathology of binge eating disorder (BED). Later stage electrophysiological potentials (P300, late positive potential) present promising markers of motivated attention with high temporal, albeit low spatial resolution. Complementing this, the N2pc is an earlier-latency component providing the possibility of more directly analyzing visuospatial attention. Therefore, we tested a group with BED (N = 60), as well as an overweight (OW; N = 28) and normal weight (NW; N = 30) group without BED in a Go/No-Go paradigm using food and nonfood distractor images. Only the OW group in exclusively the Go trials displayed a stronger spatial attention allocation towards nonfood distractors as evidenced by an increased N2pc amplitude. In the P300's time window, the OW group displayed no attentional bias towards food and the NW group only did so in the absence of a target. Solely the BED group allocated more motivated attention towards food distractors both in Go and No-Go trials. In the following late positive potential (LPP), the OW group exhibited a general attentional bias towards food distractors, while the BED group only did so in the absence of a target. These results are discussed in light of the incentive sensitization theory and a potential early attentional suppression of potent distractors.
Trifold origin of the reptilian ear ossicle and its relation to the evolutionary modification of the temporal skull region
2024-09-19

Abstract Whereas mammals are characterized by the presence of three middle ear ossicles, reptiles have only one, the columella (stapes). Nevertheless, there is a great diversity of columellar anatomy among sauropsids, especially in the unique and cartilaginous “extracolumella”‐portion. Molecular studies revealed the “columella” of chicken and quails to be formed within the second pharyngeal arch, although conflicting evidence exists for the columellar footplate and distal parts of the columella in these birds. We studied columellar development in four turtles, one lizard, and one caiman species and argue, using early blastematous stages, that, distally, the so‐called “extracolumella” in turtles is mainly of quadrate, that is, first pharyngeal arch origin. Differently, the dorsal aspect of the “extracolumella” of the lizard and a part of the “dorsal columella process” of the caiman are likely quadrate‐derived. This indicates only a partial homology of the distal columellar compartments among reptiles. Moreover, we observed in most species that, at early stages, the footplate differentiates from the otic capsule, which confirms widespread experimental findings of mesodermal cells contributing to the proximal part of the columella. We provide a hypothetical framework for the changes in the columella and quadrate morphology in reptilian evolution. Originally, as evidenced by the fossil record, the columella served as a stabilizing brace between the quadrate and braincase. Associated with changes in the feeding mode of late Permian taxa, the quadrate was integrated along the stress flows from biting, and in early development part of the quadrate differentiated to differently contribute to the distal part of the “columella‐complex,” which now contacts the tympanic membrane. In addition, part of the original otic capsule contributes to the footplate of the mobile columella, providing a connection with the inner ear.
Effects of intermittent theta burst stimulation add-on to dialectical behavioral therapy in borderline personality disorder: results of a randomized, sham-controlled pilot trial
2024-09-19

Abstract Dialectical behavioral therapy (DBT) and repetitive transcranial magnetic stimulation (rTMS) are both effective in borderline personality disorder (BPD). We hypothesized that intermittent theta burst stimulation (iTBS), a modified rTMS protocol that provides unilateral stimulation to the left dorsolateral prefrontal cortex, would enhance the effects of DBT and reduce BPD-specific symptoms more than sham stimulation. We performed a single-blind, randomized, sham-controlled pilot study to evaluate iTBS as an add-on to 8-week DBT for BPD in routine inpatient treatment. A total of 53 BPD patients were randomly assigned to either iTBS (n = 25) or sham stimulation (n = 28) in weeks 4–8 of DBT; 40 patients were eligible for inclusion in the analyses according to pre-specified criteria (≥ 16 of 20 iTBS sessions). The primary endpoint was change on the 23-item Borderline Symptom List; secondary endpoints were changes in depressive symptoms and general level of functioning. A mixed model repeated measures analysis with a 2 × 2 factorial between-subjects design showed no significant effect of add-on iTBS treatment, but a distinct trend was observed in favor of iTBS (Cohen’s d = 0.23 for group difference). We found a main effect of DBT with and without iTBS over time, indicating efficacy of 8 weeks’ DBT (d = 0.89–1.12). iTBS may be beneficial as an add-on to DBT in the long term and warrants further evaluation in larger studies. Trial registration Registered at drks.de (no. DRKS00020413) on January 13, 2020.
Interplay of aging and practice in conflict processing: A big-data diffusion-model analysis.
2024-09-19

We are continually required to exercise cognitive control in order to separate relevant and irrelevant information. Previous studies have produced mixed results as to whether cognitive control declines across adulthood and improves with practice. Moreover, little is known about the influences of aging and practice on the automatic and controlled processes underlying performance in conflict situations. This calls for analyses of extensive data using process models for conflict tasks, akin to earlier drift-diffusion model analyses of performance in cognitive nonconflict tasks. Thus, to understand how aging and practice influence cognitive control at the process level, we analyzed a large-scale data set (1,800 participants aged 21-80 years completing 60 blocklike online games of an arrow-based Eriksen flanker task). At the coarse-grained level of mean response times, the congruency effect increased across adulthood and decreased with practice following an initial increase. The finer-grained distributional response time and error rate data were closely fitted by the diffusion model for conflict tasks, which captures the dynamic interplay of automatic and controlled processing. Best-fitting parameter values revealed multiple, partially counteracting influences of aging and practice: Aging across adulthood slowed down both controlled and automatic processing (besides slowing down nondecisional processes and increasing decision caution). By contrast, practice selectively speeded up controlled processing (besides speeding up nondecisional processes and decreasing decision caution). Taken together, these findings suggest that aging and practice primarily alter the speed of controlled (aging and practice) and automatic processing (aging), rather than causing inhibitory adjustments in the strength of automatic processing. (PsycInfo Database Record (c) 2025 APA, all rights reserved).
Synthesis, electrochemical properties, and antioxidant activity of sterically hindered catechols with 1,3,4-oxadiazole, 1,2,4-triazole, thiazole or pyridine fragments
2024-09-19

A series of new RS−, RS−CH 2 − and R 2 N−CH 2 -functionalized сatechols with heterocyclic fragments such as 1,3,4-oxadiazole, 1,2,4-triazole, thiazole, or pyridine were synthesized by the reaction of 3,5-di- tert -butyl- o -benzoquinone or 3,5-di- tert -butyl-6-methoxymethylcatechol with different heterocyclic thiols. The S-functionalized catechols were prepared by the Michael reaction from 3,5-di- tert -butyl- o -benzoquinone and the corresponding thiols. The starting reagents such as substituted 1,3,4-oxadiazole-2-thiols and 4 H -triazole-3-thiols are characterized by thiol–thione tautomerism, therefore their reactions with 3,5-di- tert -butyl-6-methoxymethylcatechol can proceed at the sulfur or nitrogen atom. In the case of mercapto-derivatives of thiazole or pyridine, this process leads to the formation of the corresponding thioethers with a methylene linker. At the same time, thiolated 1,3,4-oxadiazole or 1,2,4-triazole undergo alkylation at the nitrogen atom in the reaction with 3,5-di- tert -butyl-6-methoxymethylcatechol to form the corresponding thiones. The yield of reaction products ranges from 42 to 80%. The crystal structures of catechols with 3-nitropyridine or 1,3,4-oxadiazole-2(3 H )-thione moieties were established by single-crystal X-ray analysis. The possibility of forming intra- and intermolecular hydrogen bonds has been established for these compounds. The electrochemical behavior of the studied compounds is influenced by several factors: the nature of the heterocycle and its substituents, the presence of a sulfur atom in the catechol ring, or a thione group in the heterocyclic core. The radical scavenging activity and antioxidant properties were determined using the reaction with synthetic radicals, the cupric reducing antioxidant capacity assay, the inhibition process of superoxide radical anion formation by xanthine oxidase, and the process of lipid peroxidation of rat liver ( Wistar ) homogenates in vitro.