Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel spectroscopic window on conical intersections in biomolecules

In PNAS, Keefer et al. propose an experimental approach which allows visualizing in detail the dynamics of a molecule as it passes a conical intersection (CI), that is, a real crossing point between two electronic states (1). In order to describe the photoinduced dynamics of molecules one needs to solve the time-dependent Schrodinger equation for a complex wavefunction which depends on many electronic and nuclear degrees of freedom. To simplify the problem, one typically adopts the Born–Oppenheimer approximation, which consists of separating the electronic and the nuclear coordinates in the wavefunction. This approximation, which is justified by the much higher speed of the electrons with respect to the nuclei, consists of solving the Schrodinger equation for the electrons at given fixed nuclear positions and then obtaining the electronic energies as a function of those fixed nuclear coordinates, the so-called potential energy surfaces (PES), in what is often referred to as the adiabatic approximation. In many molecules, however, there are regions of the potential energy landscape, such as CIs, where the electronic and nuclear degrees of freedom become strongly mixed and the Born–Oppenheimer (adiabatic) approximation breaks down. CIs are ubiquitous features in the photophysics and photochemistry of molecules and can be considered as “doorways” through which the photoexcited wavepacket (WP) is efficiently funneled to a lower-energy electronic state (2, 3), thus accounting for efficient nonradiative relaxation (also called internal conversion). CIs are topologies of the PES for which two or more electronic states become isoenergetic, forming a multidimensional “seam” (Fig. 1). Depending on the topography around the seam, CIs can be classified as “sloped” or “peaked. ” In a peaked CI (Fig. 1, Left ) the WP is guided to the intersection seam regardless of the initial approach direction, resulting in a more efficient conversion and triggering photochemistry. In a sloped … [↵][1]1To whom correspondence may be addressed. Email: giulio.cerullo{at}polimi.it. [1]: #xref-corresp-1-1
Ethnic Disparities in the Diagnosis of Autism in Southern Israel

The prevalence of autism spectrum disorder (ASD) is continuously rising worldwide, with remarkable differences in ASD rates being reported across ethnic and socioeconomic groups. We conducted a prospective cohort study to identify the reasons for differences in ASD rates between the Bedouin and Jewish populations in southern Israel. Screening, referral, and diagnosis of toddlers aged 16–36 months were compared between Bedouin and Jewish populations. ASD screening was conducted at 35 randomly selected mother and child health centers (MCHCs) by trained nurses using the Modified Checklist for Autism in Toddlers with follow‐up (M‐CHAT/F) instrument. Toddlers screened positive at the MCHCs were monitored throughout the referral and diagnosis process at a single medical center until a diagnosis was determined by a physician specialist using DSM‐5 criteria. The study cohort comprised 3,343 toddlers (996 Jewish and 2,347 Bedouin). Bedouin toddlers, compared to Jewish toddlers, were less likely to screen positive with M‐CHAT/F (3.0% vs. 3.9%; P = 0.165), were significantly less likely to begin the hospital diagnosis process (HR = 0.38, 95% CI: 0.14–1.08; P = 0.068), and had a higher rates of loss‐to‐follow‐up during the hospital diagnosis process (42.9% vs. 15.6%, respectively; P = 0.001). The results suggest that ethnic‐specific barriers in the diagnosis process of ASD contribute to under‐diagnosis of ASD in the Bedouin population. Facilitating the diagnosis process for Bedouin families will help to identify more children with ASD at earlier ages and consequently close the ethnic gap in ASD rates.
Remarks on horinzontal and vertical distribution of family Gadidae, Lotidae and Phycidae representatives in the eastern Adriatic.

The presence of four genera, four species and one subspecies of family Gadidae, two genera and four species of family Lotidae and two genera and two species of family Phycidae was established with certainty for the Adriatic. These families include species of different distribution in the Adriatic and of different ecological preferences. Some of these species are common and abundant fishes in the Adriatic Sea while some are rare with a very restricted distribution area. The species Trisopterus minutus is most widespread in the Adriatic, followed by Merlangius merlangus found in all shallower areas (particularly the northern Adriatic area), and Micromesistius poutassou, Phycis phycis, Phycis blennoides and Gaidropsarus mediterraneus mainly in the middle and southern Adriatic. Molva macrophthalma is however distributed only in the southern Adriatic. Of all the species in concerning, six show bathyphilous trend, distributed mainly in the area of continental slope or bathyal (bellow 200 m depth) and four species occur almost exclusively in the area of continental shelf that is down to 200 m. As to the substratum, most of the species prefer muddy bottoms rather than sandy and muddy – sandy bottoms.
Gut Microbiota: the Emerging Link to Lung Homeostasis and Disease

The gut microbiota plays a crucial role in the development of the immune system and confers benefits or disease susceptibility to the host. Emerging studies have indicated the gut microbiota could aﬀect pulmonary health and disease through cross talk between the gut microbiota and the lungs. Gut microbiota dysbiosis could lead to acute or chronic lung disease, such as asthma, tuberculosis, and lung cancer. In addition, the composition of the gut microbiota may be associated with different lung diseases, the prevalence of which also varies by age. ABSTRACT The gut microbiota plays a crucial role in the development of the immune system and confers benefits or disease susceptibility to the host. Emerging studies have indicated the gut microbiota could aﬀect pulmonary health and disease through cross talk between the gut microbiota and the lungs. Gut microbiota dysbiosis could lead to acute or chronic lung disease, such as asthma, tuberculosis, and lung cancer. In addition, the composition of the gut microbiota may be associated with different lung diseases, the prevalence of which also varies by age. Modulation of the gut microbiota through short-chain fatty acids, probiotics, and micronutrients may present potential therapeutic strategies to protect against lung diseases. In this review, we will provide an overview of the cross-talk between the gut microbiota and the lungs, as well as elucidate the underlying pathogenesis and/or potential therapeutic strategies of some lung diseases from the point of view of the gut microbiota.
Post-Transcriptional Expression Control in Platelet Biogenesis and Function

Platelets are highly abundant cell fragments of the peripheral blood that originate from megakaryocytes. Beside their well-known role in wound healing and hemostasis, they are emerging mediators of the immune response and implicated in a variety of pathophysiological conditions including cancer. Despite their anucleate nature, they harbor a diverse set of RNAs, which are subject to an active sorting mechanism from megakaryocytes into proplatelets and affect platelet biogenesis and function. However, sorting mechanisms are poorly understood, but RNA-binding proteins (RBPs) have been suggested to play a crucial role. Moreover, RBPs may regulate RNA translation and decay following platelet activation. In concert with other regulators, including microRNAs, long non-coding and circular RNAs, RBPs control multiple steps of the platelet life cycle. In this review, we will highlight the different RNA species within platelets and their impact on megakaryopoiesis, platelet biogenesis and platelet function. Additionally, we will focus on the currently known concepts of post-transcriptional control mechanisms important for RNA fate within platelets with a special emphasis on RBPs.
Tumor invasion in the central airway is a risk factor for early‐onset checkpoint inhibitor pneumonitis in patients with non‐small cell lung cancer

Anti‐programmed death‐1 (PD‐1) immunotherapy can cause immune‐related pneumonitis, also known as checkpoint inhibitor pneumonitis (CIP). CIP that develops early after the initiation of anti‐PD‐1 immunotherapy is important because it is more severe than CIP that develops later. However, only a few studies have examined the risk factors for early‐onset CIP. Previous studies have reported several risk factors for CIP, including imaging findings of airway obstruction adjacent to lung tumors. However, the utility of this factor is debatable. Therefore, we investigated potential risk factors for early‐onset CIP, including tumor invasion in the central airway (TICA), in patients with non‐small cell lung cancer (NSCLC) receiving anti‐PD‐1 therapy.
Acrylonitrile, Addendum [BAT Value Documentation, 2010]

To determine the parameter N-(Cyanoethyl)valine, a reliable GC-MS method is available. The detection limit for that method is 0.3 μg N-(Cyanoethyl)valine/l blood (Van Sittert 1996). For the investigation, 10 ml venous blood stabilized with EDTA is required. There is no fixed time for sampling. Once the sample has been taken, the blood has to be centrifuged and the plasma withdrawn. The isolated erythrocytes can be kept for three days in a refrigerator or deep frozen at -20 °C. Correlations between external and internal exposure
Evolutionary dynamics of genome size in a radiation of woody plants.

PREMISE Plant genome size ranges widely, providing many opportunities to examine how genome size variation affects plant form and function. We analyzed trends in chromosome number, genome size, and leaf traits for the woody angiosperm clade Viburnum to examine the evolutionary associations, functional implications, and possible drivers of genome size. METHODS Chromosome counts and genome size estimates were mapped onto a Viburnum phylogeny to infer the location and frequency of polyploidization events and trends in genome size evolution. Genome size was analyzed with leaf anatomical and physiological data to evaluate the influence of genome size on plant function. RESULTS We discovered nine independent polyploidization events, two reductions in base chromosome number, and substantial variation in genome size with a slight trend toward genome size reduction in polyploids. We did not find strong relationships between genome size and the functional and morphological traits that have been highlighted at broader phylogenetic scales. CONCLUSIONS Polyploidization events were sometimes associated with rapid radiations, demonstrating that polyploid lineages can be highly successful. Relationships between genome size and plant physiological function observed at broad phylogenetic scales may be largely irrelevant to the evolutionary dynamics of genome size at smaller scales. The view that plants readily tolerate changes in ploidy and genome size, and often do so, appears to apply to Viburnum.
Avaliação genética e fenotípica de características de conformação em potros de três raças eqüinas

Foram utilizadas mensuracoes de 418 potros das racas Quarto de Milha, Mangalarga e Arabe, com o objetivo de estimar herdabilidades e correlacoes geneticas e fenotipicas entre caracteristicas de conformacao por meio da metodologia da maxima verossimilhanca restrita. 4 arquivo de pedigree era composto de 3.4Q8 animais. Os efeitos das covariaveis grau de endogamia do potro, idade da egua ao parto, duracao do periodo de gestacao e idade a mensuracao sobre estas estimativas foram avaliados. Consideraram- se tambem como efeitos fixos rebanho, estacao, ano de nascimento, grupo genetico e sexo. Nos animais com idade media de 194 dias, foram feitas as seguintes mensuracoes: altura na cernelha, perimetro toracico, perimetro da canela, comprimento da corpo e peso corporal. As medias, os mos-padrao e as respectivas herdabilidades (h2 ), sem o ajuste de covariavel, foram: 125,11 ± 0,16 cm e 0,43 parai altura da cernelha; I 3 ,34 ±a,3t} cm e 0,54 para perimetro toracico; 16,68 ± U,04 cm e Ci,38 para perimetro da canela; 121,9I ± 0,20 cm e 0,20 para comprimento do corpo e 1 g0,Z5 ± I ,06 kg e ta,o l para peso corporal.Foram observadas pequenas vadacoes nos valores estimados de h7 de todas as caracteristicas, com a inclusao de covariaveis no modelo. Comportamento similar foi observado na analise bicaracteristica. As correlacoes geneticas (r) e fenotfpicas C rp ) entre as caracteristicas foram, respectivamente, altura da cernelha e perfinetro toracico (0,58; x,69), altura da cernelha e perfrnetro da canela (0,87; 0,64), altura da cernelha e comprimento da corpo (u,97; 0,79), altura da cerneiha e piso corporal (0,37; 0,63), perirnetro toracico e perlmetro da canela (1,00= O , 66) , perimetro toracica e comprimento elo corpo (0,6 1 ; 0,7Q), perimetro toracico e peso corporal (1,U0; Q,99), perimetro da canela e comprimento do corpo (0,86; 0,6u), perimetro da canela e peso corporal (1,Q0; 0,68) e comprimento do corpo e peso corporal (0,61; 0,67). Pouca variacao foi encontrada nas estimativas de ~ e F,, com a iric1uso de covariaveis no modelo.
Demonstration of a Filterless, Multi-Point, and Temperature-Independent Fiber Bragg Grating Dynamical Demodulator Using Pulse-Width Modulation

We demonstrated in this work a filterless, multi-point and temperature-independent FBG (fiber Bragg grating) dynamical demodulator using pulse-width-modulation (PWM). In this approach, the FBG interrogation system is composed of a tunable laser and a demodulator that is designed to detect the wavelength shift of the FBG sensor without any optical filter making it very suitable to be used in harsh environments. In this work, we applied the proposed method that uses the PWM technique for FBG sensors placed in high pressure and high-temperature environments. The proposed method was characterized in the laboratory using an FBG sensor modulated in a frequency of 6 Hz, with a 1 kHz sweeping frequency in the wavelength range from 1527 to 1534 nm. Also, the method was evaluated in a field test in an engine of a thermoelectric power plant.
Crotonases: Nature’s Exceedingly Convertible Catalysts

The crotonases comprise a widely distributed enzyme superfamily that has multiple roles in both primary and secondary metabolism. Many crotonases employ oxyanion hole-mediated stabilization of intermediates to catalyze the reaction of coenzyme A (CoA) thioester substrates (e.g., malonyl-CoA, α,β-unsaturated CoA esters) both with nucleophiles and, in the case of enolate intermediates, with varied electrophiles. Reactions of crotonases that proceed via a stabilized oxyanion intermediate include the hydrolysis of substrates including proteins, as well as hydration, isomerization, nucleophilic aromatic substitution, Claisen-type, and cofactor-independent oxidation reactions. The crotonases have a conserved fold formed from a central β-sheet core surrounded by α-helices, which typically oligomerizes to form a trimer or dimer of trimers. The presence of a common structural platform and mechanisms involving intermediates with diverse reactivity implies that crotonases have considerable potential for biocatalysis.
Effects of yeast strain on anthocyanin, color, and antioxidant activity of mulberry wines

In this study, the effects of yeast strains on anthocyanin, color, and antioxidant activity of mulberry wines were investigated. Principal component analysis (PCA) were used to evaluate differences among the five mulberry wines. Results showed that yeast strains have a significant effect on anthocyanin, color, and antioxidant activity of mulberry wines. The total phenol content in mulberry wines were 145.42–197.65 mg gallic acid equivalents/100 mL. Cyanidin-3-O-glucoside (C3G) and cyanidin-3-O-rutinoside (C3R) were two major anthocyanins in mulberry wine. The C3G contents ranged from 3.56 to 7.69 mg/100 mL, while C3R ranged from 4.28 to 8.38 mg/100 mL. Total phenol content, total flavonoids content and antioxidant activity in mulberry wine fermented by yeast SY were significantly higher (p < .05) than the other wines. Two principal components accounted for 88.31% of total variance. Results of PCA indicated that these five mulberry wines could differentiated by anthocyanin, color, and antioxidant activity. Practical applications This study was undertaken, in order to further examine the effects of different yeast strains on the anthocyanin, color, and antioxidant activity of mulberry wines. An appropriate yeast strain may help reducing anthocyanin degradation in mulberry wine during fermentation, avoiding a dramatic impact on its color and protecting the beneficial effects of these biologically active compounds on human health. Finally, mulberry wines will provide a new perspective for winemakers and will become alternative functional food for health-conscious consumers in the future.
Physical Fitness and Apolipoprotein E Genotype Influence Cortical Networking and Intelligence in Adolescents

AIMS This study examined the interactive effect of physical fitness and Apolipoprotein e4 on intelligence and cortical networking in adolescents. METHODS Participants were middle school students consisting of 10 and 8 high- and low-fit e4 carriers (e4+), respectively, and 14 and 10 high- and low-fit non-carriers (e4−), respectively. Inter- and intra-hemispheric coherences were calculated to examine cortico-cortical communication during intelligence test. RESULTS Coherence in low-fit e4+ was lower than in high-fit e4+, while coherence in low-fit e4− was similar to or higher than in high-fit e4−. CONCLUSION The presence of the e4 allele can decrease neural networking 50–60 years before Alzheimer’s disease onset: however, physical fitness may compensate for the negative impact of genotype. Moreover, the beneficial effects of physical fitness may differ depending on functional states of the adolescent brain according to the presence of the e4 allele.
Diffusion MRI tractography filtering techniques change the topology of structural connectomes

Objective. The use of non-invasive techniques for the estimation of structural brain networks (i.e. connectomes) opened the door to large-scale investigations on the functioning and the architecture of the brain, unveiling the link between neurological disorders and topological changes of the brain network. This study aims at assessing if and how the topology of structural connectomes estimated non-invasively with diffusion MRI is affected by the employment of tractography filtering techniques in structural connectomic pipelines. Additionally, this work investigates the robustness of topological descriptors of filtered connectomes to the common practice of density-based thresholding. Approach. We investigate the changes in global efficiency, characteristic path length, modularity and clustering coefficient on filtered connectomes obtained with the spherical deconvolution informed filtering of tractograms and using the convex optimization modelling for microstructure informed tractography. The analysis is performed on both healthy subjects and patients affected by traumatic brain injury and with an assessment of the robustness of the computed graph-theoretical measures with respect to density-based thresholding of the connectome. Main results. Our results demonstrate that tractography filtering techniques change the topology of brain networks, and thus alter network metrics both in the pathological and the healthy cases. Moreover, the measures are shown to be robust to density-based thresholding. Significance. The present work highlights how the inclusion of tractography filtering techniques in connectomic pipelines requires extra caution as they systematically change the network topology both in healthy subjects and patients affected by traumatic brain injury. Finally, the practice of low-to-moderate density-based thresholding of the connectomes is confirmed to have negligible effects on the topological analysis.
Ovarian surface epithelium of hypothyroid newborn and neonatal rats: From proliferating cell nuclear antigen and caspase-3 perspectives

Introduction. The ovarian surface epithelium (OSE) undergoes intensive regeneration and remodelling after each ovulation during the whole reproductive period. This process increases the risk of one of the most common ovarian tumors in women and the female dog. Considering the fact that maternal hypothyroidism highly impacts cell proliferation and cell death during folliculogenesis in the early neonatal period, we aimed to analyze its effect on OSE morphology and dynamics. Materials and Methods. The study was performed on newborn (24-h-old) and neonatal (4-day-old) female rats, a randomized trial between the control and hypothyroid groups, born under controlled circumstances and hypothyroid mothers, respectively. Their ovaries were analyzed histologically and processed to determine the OSE cell height as an average value of four measurement points. Also, the immunopositivity of the proliferating cell nuclear antigen (PCNA) and caspase-3 were assessed semiquantitatively. Results and Conclusions. No major structural differences of OSE were found between groups within the given ages except for a slight increment of OSE cell height and incompleteness of apical cell membrane with cytoplasmic projections in hypothyroid animals. PCNA immunopositivity of the OSE cells was higher in ovaries of hypothyroid animals of both ages in comparison to the controls. Moreover, only scarce OSE cells were caspase-3 positive in both groups and ages, with no difference in immunopositivity. Our study confirms the impact of hypothyroidism in the early postnatal period on morphology and proliferation rate of OSE cells, with no effect on caspase-3 dependent cell removal, which may serve as a premise for future investigation of potential carcinogenesis, in terms of prevention and treatment of ovarian cancer.
Vascular Flora of Longleaf Pine Woodlands after Wind Disturbance and Salvage Harvesting in the Alabama Fall Line Hills

ABSTRACT The Oakmulgee District of the Talladega National Forest is the largest remnant of the endangered longleaf pine (Pinus palustris) ecosystem in Alabama. A partial floristic survey using nested plots and survey plots was conducted May–July 2016 in longleaf pine woodlands of the Oakmulgee District that were differentially impacted by a 27 April 2011 EF3 tornado and a subsequent salvage harvesting operation. Vascular plants were identified and ranked by frequency of occurrence (rare, occasional, common, and abundant) in three disturbance categories: undisturbed, wind-disturbed, and compound-disturbed (wind-disturbed and salvage-harvested). Overall, 192 plant taxa in 68 families and 137 genera were documented. Plant taxonomic richness was lowest on undisturbed sites (90 taxa), greatest on wind-disturbed sites (160 taxa), and reduced on compound-disturbed sites (126 taxa). Although salvage harvesting reduced taxonomic richness, 46 of the 48 plant taxa unique to unharvested wind-disturbed sites were rare (occurred on <10% of nested plots). Moreover, undisturbed sites had only nine unique taxa, of which eight were rare. Decisions on whether to salvage harvest must consider the ecological significance of these rare plants. Wind- and compound-disturbed areas may recover toward predisturbance conditions, and the floristic list presented here provides the baseline to monitor this succession. The documented floristic composition also provides insight on short-term responses of vascular plants to differential disturbance impacts in an understudied region of the longleaf pine ecosystem.