Miracle-dz/UniFAR-FTUs huggingface dataset:
Controlled modulation of the dynamics of the Deinococcus grandis Dps N‐terminal tails by divalent metals

DNA‐binding proteins from starved cells (Dps) are small multifunctional nanocages expressed by prokaryotes in acute oxidative stress conditions or during the starvation‐induced stationary phase, as a bacterial defense mechanism. Dps proteins protect bacterial DNA from damage by either direct binding or by removing precursors of reactive oxygen species from solution. The DNA‐binding properties of most Dps proteins studied so far are related to their unordered, flexible, N‐ and C‐terminal extensions. In a previous work, we revealed that the N‐terminal tails of Deinoccocus grandis Dps shift from an extended to a compact conformation depending on the ionic strength of the buffer and detected a novel high‐spin ferrous iron center in the proximal ends of those tails. In this work, we further explore the conformational dynamics of the protein by probing the effect of divalent metals binding to the tail by comparing the metal‐binding properties of the wild‐type protein with a binding site‐impaired D34A variant using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism, and small‐angle X‐ray scattering. The N‐terminal ferrous species was also characterized by Mössbauer spectroscopy. The results herein presented reveal that the conformation of the N‐terminal tails is altered upon metal binding in a gradual, reversible, and specific manner. These observations may point towards the existence of a regulatory process for the DNA‐binding properties of Dps proteins through metal binding to their N‐ and/or C‐terminal extensions.
Global soil nitrogen cycle pattern and nitrogen enrichment effects: Tropical versus subtropical forests

Tropical and subtropical forest biomes are a main hotspot for the global nitrogen (N) cycle. Yet, our understanding of global soil N cycle patterns and drivers and their response to N deposition in these biomes remains elusive. By a meta‐analysis of 2426‐single and 161‐paired observations from 89 published 15 N pool dilution and tracing studies, we found that gross N mineralization (GNM), immobilization of ammonium ( INH4 ) and nitrate ( INO3 ), and dissimilatory nitrate reduction to ammonium (DNRA) were significantly higher in tropical forests than in subtropical forests. Soil N cycle was conservative in tropical forests with ratios of gross nitrification (GN) to INH4 (GN/ INH4 ) and of soil nitrate to ammonium (NO3−/NH4+) less than one, but was leaky in subtropical forests with GN/ INH4 and NO3−/NH4+ higher than one. Soil NH4+ dynamics were mainly controlled by soil substrate (e.g., total N), but climatic factors (e.g., precipitation and/or temperature) were more important in controlling soil NO3− dynamics. Soil texture played a role, as GNM and INH4 were positively correlated with silt and clay contents, while INO3 and DNRA were positively correlated with sand and clay contents, respectively. The soil N cycle was more sensitive to N deposition in tropical forests than in subtropical forests. Nitrogen deposition leads to a leaky N cycle in tropical forests, as evidenced by the increase in GN/ INH4 , NO3−/NH4+, and nitrous oxide emissions and the decrease in INO3 and DNRA, mainly due to the decrease in soil microbial biomass and pH. Dominant tree species can also influence soil N cycle pattern, which has changed from conservative in deciduous forests to leaky in coniferous forests. We provide global evidence that tropical, but not subtropical, forests are characterized by soil N dynamics sustaining N availability and that N deposition inhibits soil N retention and stimulates N losses in these biomes.
The superficial peroneal neurocutaneous flap: a cadaveric study

Abstract Soft tissue defects around the ankle are common and must be covered with thin and pliable flaps. A regional flap, particularly from the dorsum of the foot was considered ideal. A neurocutaneous flap, based on the superficial peroneal nerve (SPN) and its branches was designed as a proximally based flap via cadaveric dissection. This study aimed to demonstrate the vascularity and characteristics of the superficial peroneal neurocutaneous (SPNC) flap. The SPNC flap was created in 11 lower limbs (seven cadavers) using a proximally based design. The skin flap was dissected at the dorsum of the foot, followed by injection of diluted methylene blue through the anterior tibial artery, to visualize the vascularity. The flap pedicle above the anterior ankle joint line was dissected along the SPN for anatomical study of perforating branches, paraneural vessels, and flap territory. The mean distances of the most proximal perforating branches were 1.51 ± 1.48 cm from the anterior ankle joint line, and 5.12 ± 1.78 cm from the lateral malleolus. The mean distances of the most distal perforating branches were 2.75 ± 1.54 cm from the anterior ankle joint line, and 5.90 ± 1.81 cm from the lateral malleolus. The mean number of perforating branches was 3.73 ± 1.49. The mean flap territories were 5.51 ± 0.59 cm in length, and 7.15 ± 0.64 cm in width. The SPNC flap is an alternative method for soft tissue reconstruction around the ankle with a proximally based flap design. The antegrade flow has been shown to offer effective vascularity in flaps prepared via cadaveric dissection.
A prognostic model for predicting the duration of 20,049 sickness absence spells due to shoulder lesions in a population-based cohort in Sweden

Main objective Sickness absence duration for shoulder lesion patients is difficult to prognosticate, and scientific evidence for the sick-listing practice is lacking. Our objective was to develop a clinically implementable prediction model for the duration of a sickness absence spell due to shoulder lesions. Methods All new sickness absence spells due to shoulder lesions (ICD-10-code: M75) issued in the period January 2010—June 2012 that were longer than 14 days were identified through the nationwide sickness absence insurance register. Information on predictors was linked from four other nationwide registers. Piecewise-constant hazards regression models were fitted to predict duration of sickness absence. The model was developed and validated using split sample validation. Variable selection was based on log-likelihood loss ranking when excluding a variable from the model. The model was evaluated using calibration plots and the c-statistic. Results 20 049 sickness absence spells were identified, of which 34% lasted >90 days. Predictors included in the model were age, sex, geographical region, occupational status, educational level, birth country, specialized healthcare at start of the spell, number of sickness absence days in the last 12 months, and specialized healthcare the last 12 months, before start date of the index sickness absence spell. The model was satisfactorily specified and calibrated. Overall c-statistic was 0.54 (95% CI 0.53–0.55). C-statistic for predicting durations >90, >180, and >365 days was 0.61, 0.66, and 0.74, respectively. Significance The model can be used to predict the duration of sickness absence due to shoulder lesions. Covariates had limited predictive power but could discriminate the very long sickness absence spells from the rest.
A gaze-contingent saccadic re-referencing training with simulated central vision loss

Patients with central vision loss (CVL) adopt an eccentric retinal location for fixation, a preferred retinal location (PRL), to compensate for vision loss at the fovea. Although most patients with CVL are able to rapidly use a PRL instead of the fovea, saccadic re-referencing to a PRL develops slowly. Without re-referencing, saccades land the saccade target in the scotoma. This results in corrective saccades and leads to inefficient visual exploration. Here, we tested a new method to train saccadic re-referencing. Healthy participants performed gaze-contingent visual search tasks with simulated central scotoma in which participants had to fixate targets with an experimenter-defined forced retinal location (FRL). In experiment 1, we compared single-target search and foraging search tasks in the course of five training sessions. Results showed that both tasks improved the efficiency of gaze sequences and led to saccadic re-referencing to the FRL. In experiment 2, we trained participants extensively for 25 sessions, both with and without a gaze-contingent FRL-marker visible during training. After extensive training, observers’ performance approached that of foveal vision. Thus, gaze-contingent FRL-fixation may become an efficient tool for saccadic re-referencing training in patients with central vision loss.
Calorie restriction alters the mechanisms of radiation-induced mouse thymic lymphomagenesis

Calorie restriction (CR) suppresses not only spontaneous but also chemical- and radiation-induced carcinogenesis. Our previous study revealed that the cancer-preventive effect of CR is tissue dependent and that CR does not effectively prevent the development of thymic lymphoma (TL). We investigated the association between CR and the genomic alterations of resulting TLs to clarify the underlying resistance mechanism. TLs were obtained from previous and new experiments, in which B6C3F1 mice were exposed to radiation at 1 week of age and fed with a CR or standard (non-CR) diet from 7 weeks throughout their lifetimes. All available TLs were used for analysis of genomic DNA. In contrast to the TLs of the non-CR group, those of the CR group displayed suppression of copy-neutral loss of heterozygosity (LOH) involving relevant tumor suppressor genes (Cdkn2a, Ikzf1, Trp53, Pten), an event regarded as cell division–associated. However, CR did not affect interstitial deletions of those genes, which were observed in both groups. In addition, CR affected the mechanism of Ikzf1 inactivation in TLs: the non-CR group exhibited copy-neutral LOH with duplicated inactive alleles, whereas the CR group showed expression of dominant-negative isoforms accompanying a point mutation or an intragenic deletion. These results suggest that, even though CR reduces cell division–related genomic rearrangements by suppressing cell proliferation, tumors arise via diverse carcinogenic pathways including inactivation of tumor suppressors via interstitial deletions and other mutations. These findings provide a molecular basis for improved prevention strategies that overcome the CR resistance of lymphomagenesis.
Resampling Plan Using Orthogonal Array and Its Application to Influence Analysis

推 定量 の偏 り,分 散,さ らに一 般的 な誤 差 の尺度 を ノンパ ラメ トリックに推 定す るた め に,ジ ャ ック ナイ フ法,ブ ー トス トラ ップ法 な ど様 々な リサ ンプ リ ング方式 が提 案 されて い る,本 稿 で は,ジ ャ ックナイ フ法 に関 連 した直 交配列 表 を 用 いた リサ ンプ リング方 式 とそ の影響 分析 への応 用 につ いて提 案す る. こ の リサ ン プ リング方 式 の基 にな るの は,Hartigan(1969)のTypical Value Theoremで あ り,本 方 式で得 られ る リサ ンプルはtypical setを 形成 し,か つ 釣合 型 とな る. ま た,本 方式 に よる影 響分 析で は,個 々の観測値 が注 目す る統 計量 に与 え る影 響 を,分 散 分析 の加法 モ デル に よ り主 効果 と交 互作用 として と らえ る点 に特徴 が あ る. 2つ の数 値例 を通 じて その実 用性 を検 証す る.
More Kindness, Less Prejudice against Immigrants? A Preliminary Study with Adolescents

Prejudice against immigrants is a relevant research topic within social psychology. Researchers identified several individual variables affecting anti-immigrant prejudice, such as morality and personality. However, until now, prejudice has never been studied in relation to kindness, which might be a significant protective factor against prejudice. Based on Kohlberg’s theory of moral judgement, four stage dimensions of kindness were identified, from egocentric to authentic kindness (i.e., a means for social progress and improvement). This study aims to explore the relationship between the four kindness dimensions and blatant and subtle prejudice against immigrants in adolescence, by also considering the moderating role of adolescents’ sex. It involved 215 Italian participants (77% girls), who were asked to fill in a self-report questionnaire. Results showed that boys scored higher on egocentric kindness than girls, but no sex differences emerged for prejudice. Egocentric and extrinsically motivated kindness appeared to be risk factors for prejudice, whereas the most authentic form of kindness was a protective factor. In addition, adolescents’ sex moderated the relationship between egocentric kindness and blatant prejudice, whereby this association was stronger for boys. The implications of these findings, the study’s limitations, and suggestions for future research are discussed.
Theoretical modelling of scanning tunnelling microscopy, scanning tunnelling spectroscopy and atomic force microscopy

The capability of the atomic force microscope (AFM) and the scanning tunnelling microscope (STM) to image surfaces with atomic resolution is still amazing us. Theory has been for a long time and in certain respects remains to the present day in debt to experiment. The aim of this review is to describe the development of theoretical models of the AFM, which serves both as an imaging tool and as a tool for manipulating atoms and molecules at surfaces. Models based on classical and quantum mechanical treatment of tip-sample interaction in the AFM are reviewed with emphasis on the explanations of atomic resolution that they provide. The attempts to understand atomic resolution in the STM on metal surfaces started with the local charge-density concept; however, even exact theories based on three-dimensional scattering theory, using different models for the tip and the sample, cannot provide an understanding of the large corrugation amplitudes of the tip height in the constant-current scanning mode in STM on densely packed metal surfaces. A recently developed dynamic theory of STM, regarding the tunnelling as an excited-state property of the interacting tip-plus-sample system, provides an insight into the physical background of atomic resolution in these cases. Other issues in the theory of STM and scanning tunnelling spectroscopy (STS) addressed relate to the equivalence of the current-density formulation of STM theory and the generalized Ehrenfest theorem, tunnelling via surface states and resonances, the mirror theorem of STS, image reversal in STM, many-particle effects in STM. With the prospect of converting the AFM and STM into tools for surface technology on the nanoscopic scale, theory will be challenged to suggest models going beyond the single-particle approaches and the adiabatic approximation.
Calibration of the SOLSPEC Spectrometer to Measure the Solar Irradiance from Space

The SOLSPEC instrument has been built to carry out absolute solar spectral irradiance measurements from space. It was first flown in December 1983 on mission STS 9 (Spacelab 1), from August 1992 to June 1993 on board the free-flying EURECA platform with mission STS 46 (deployment) and STS 57 (retrieval), then flown three times more with the ATLAS missions STS 45, 56 and 66. Further applications are foreseen in combination with the International Space Station Alpha (ISSA). SOLSPEC covers a wavelength range from 180 nm to 3000 nm split into three separate spectrometer channels (ultraviolet, visible and infrared) and has been calibrated pre- and post-flight using a black body at the Landessternwarte Heidelberg with temperatures up to 3300 K. In this paper the calibration concept is presented, together with a short instrument description and suggestions for improvements in order that higher black-body temperatures can be reached.
Two new alkaloids from Dendrobium nobile Lindl. exhibited neuroprotective activity, and dendrobine alleviated Aβ1−42‐induced apoptosis by inhibiting CDK5 activation in PC12 cells

Dendrobium nobile Lindl. is registered in the Chinese Pharmacopoeia as a traditional medicine. Phytochemical investigation of the ethanol extract of D. nobile Lindl. stems yielded three alkaloid compounds, including two new compounds dendroxine B (2) and denrine B (3) as well as one known compound dendrobine (1). Here, we identified the structure of these compounds using spectroscopic analyses and compared them with those described in previous studies. Compounds 1–3 were found to show protective effect against amyloid‐β 1−42 (Aβ1−42)‐induced neurotoxicity in rat pheochromocytoma (PC12) cells, among which dendrobine exhibited the most significant neuroprotective effect. Hoechst 33342/propidium iodide staining indicated that dendrobine ameliorated Aβ1−42‐induced apoptosis. Moreover, quantitative real‐time polymerase chain reaction and western blot analysis analysis demonstrated that dendrobine suppressed the activation of cyclin‐dependent kinase 5 (CDK5), upregulated Bcl‐2 expression, and downregulated Bax, cyto‐c, and caspase‐3 expression. Molecular docking analysis and surface plasmon resonance assay suggested that dendrobine directly bound to CDK5 protein with a KD value of 2.05 × 10−4 M. In summary, alkaloids are the neuroprotective constituents of D. nobile Lindl. , and dendrobine protected PC12 cells against Aβ1−42‐induced apoptosis by inhibiting CDK5 activation.
The effect of procedural time on dysplasia detection rate during endoscopic surveillance of Barrett’s esophagus

Background Endoscopic surveillance of Barrett’s esophagus (BE) with Seattle protocol biopsies is time-consuming and inadequately performed in routine practice. There is no recommended procedural time for BE surveillance. We investigated the duration of surveillance procedures with adequate tissue sampling and effect on dysplasia detection rate (DDR). Methods We performed post hoc analysis from the standard arm of a crossover randomized controlled trial recruiting patients with BE (≥C2 and/or ≥M3) and no clearly visible dysplastic lesions. After inspection with white-light imaging, targeted biopsies of subtle lesions and Seattle protocol biopsies were performed. Procedure duration and biopsy number were stratified by BE length. The effect of endoscopy-related variables on DDR was assessed by multivariable logistic regression. Results Of 142 patients recruited, 15 (10.6 %) had high grade dysplasia/intramucosal cancer and 15 (10.6 %) had low grade dysplasia. The median procedural time was 16.5 minutes (interquartile range 14.0–19.0). Endoscopy duration increased by 0.9 minutes for each additional 1 cm of BE length. Seattle protocol biopsies had higher sensitivity for dysplasia than targeted biopsies (86.7 % vs. 60.0 %; P = 0.045). Longer procedural time was associated with increased likelihood of dysplasia detection on quadrantic biopsies (odds ratio [OR] 1.10, 95 %CI 1.00–1.20, P = 0.04), and for patients with BE > 6 cm also on targeted biopsies (OR 1.21, 95 %CI 1.04–1.40; P = 0.01). Conclusions In BE patients with no clearly visible dysplastic lesions, longer procedural time was associated with increased likelihood of dysplasia detection. Adequate time slots are required to perform good-quality surveillance and maximize dysplasia detection.
Classifying Alzheimer's disease and frontotemporal dementia using machine learning with cross‐sectional and longitudinal magnetic resonance imaging data

Alzheimer's disease (AD) and frontotemporal dementia (FTD) are common causes of dementia with partly overlapping, symptoms and brain signatures. There is a need to establish an accurate diagnosis and to obtain markers for disease tracking. We combined unsupervised and supervised machine learning to discriminate between AD and FTD using brain magnetic resonance imaging (MRI). We included baseline 3T‐T1 MRI data from 339 subjects: 99 healthy controls (CTR), 153 AD and 87 FTD patients; and 2‐year follow‐up data from 114 subjects. We obtained subcortical gray matter volumes and cortical thickness measures using FreeSurfer. We used dimensionality reduction to obtain a single feature that was later used in a support vector machine for classification. Discrimination patterns were obtained with the contribution of each region to the single feature. Our algorithm differentiated CTR versus AD and CTR versus FTD at the cross‐sectional level with 83.3% and 82.1% of accuracy. These increased up to 90.0% and 88.0% with longitudinal data. When we studied the classification between AD versus FTD we obtained an accuracy of 63.3% at the cross‐sectional level and 75.0% for longitudinal data. The AD versus FTD versus CTR classification has reached an accuracy of 60.7%, and 71.3% for cross‐sectional and longitudinal data respectively. Disease discrimination brain maps are in concordance with previous results obtained with classical approaches. By using a single feature, we were capable to classify CTR, AD, and FTD with good accuracy, considering the inherent overlap between diseases. Importantly, the algorithm can be used with cross‐sectional and longitudinal data.
Orbit algebras that are invariant under stable equivalences of Morita type

In this note we show that there are a lot of orbit algebras that are invariant under stable equivalences of Morita type between self-injective algebras. There are also indicated some links between Auslander-Reiten periodicity of bimodules and noetherianity of their orbit algebras.
Prepregnancy Migraine, Migraine Phenotype, and Risk of Adverse Pregnancy Outcomes

Background and Objective Migraine is a highly prevalent neurovascular disorder among reproductive-aged women. Whether migraine history and migraine phenotype might serve as clinically useful markers of obstetric risk is not clear. The primary objective of this study was to examine associations of prepregnancy migraine and migraine phenotype with risks of adverse pregnancy outcomes. Methods We estimated associations of self-reported physician-diagnosed migraine and migraine phenotype with adverse pregnancy outcomes in the prospective Nurses' Health Study II (1989–2009). Log-binomial and log-Poisson models with generalized estimating equations were used to estimate relative risks (RRs) and 95% CIs for gestational diabetes mellitus (GDM), preeclampsia, gestational hypertension, preterm delivery, and low birthweight. Results The analysis included 30,555 incident pregnancies after cohort enrollment among 19,694 participants without a history of cardiovascular disease, diabetes, or cancer. After adjusting for age, adiposity, and other health and behavioral factors, prepregnancy migraine (11%) was associated with higher risks of preterm delivery (RR = 1.17; 95% CI = 1.05–1.30), gestational hypertension (RR = 1.28; 95% CI = 1.11–1.48), and preeclampsia (RR = 1.40; 95% CI = 1.19–1.65) compared with no migraine. Migraine was not associated with low birthweight (RR = 0.99; 95% CI = 0.85–1.16) or GDM (RR = 1.05; 95% CI = 0.91–1.22). Risk of preeclampsia was somewhat higher among participants with migraine with aura (RR vs no migraine = 1.51; 95% CI = 1.22–1.88) than migraine without aura (RR vs no migraine = 1.30; 95% CI = 1.04–1.61; p-heterogeneity = 0.32), whereas other outcomes were similar by migraine phenotype. Participants with migraine who reported regular prepregnancy aspirin use had lower risks of preterm delivery (<2×/week RR = 1.24; 95% CI = 1.11–1.38; ≥2×/week RR = 0.55; 95% CI = 0.35–0.86; p-interaction < 0.01) and preeclampsia (<2×/week RR = 1.48; 95% CI = 1.25–1.75; ≥2×/week RR = 1.10; 95% CI = 0.62–1.96; p-interaction = 0.39); however, power for these stratified analyses was limited. Discussion Migraine history, and to a lesser extent migraine phenotype, appear to be important considerations in obstetric risk assessment and management. Future research should determine whether aspirin prophylaxis may be beneficial for preventing adverse pregnancy outcomes among pregnant individuals with a history of migraine.