Miracle-dz/UniFAR-FTUs huggingface dataset:
Intrinsic biotic factors and microsite conditions drive seedling survival in a species with masting reproduction

Abstract Seedling recruitment following a masting event, where more fruits are produced in synchrony and intermittently compared with other species, plays a crucial role in determining species diversity and community structure. Such seedling recruitment can be superabundant, but followed by high mortality shortly thereafter. Differences in biotic factors such as seedling characteristics, competition, and herbivory, and microsite‐specific abiotic factors could determine seedling fate in space and time. In a subtropical forest in south China, for 2 years using censuses conducted every 1–2 months, we monitored 40 seed traps and 120, 1 m2 quadrats in five 1‐ha plots located from 1,400 to 1,850 m asl for the masting maple species, Acer campbellii subsp. sinense (Pax) P.C. DeJong. We measured biotic—conspecific and heterospecific seedling density, species richness, herbivory, seedling height, and leaf number—and abiotic—canopy openness, slope, and aspect—factors to assess drivers of seedling survival and evaluated A. campbellii subsp. sinense presence in the soil seed bank (SSB). The masting seed dispersal peak and seedling emergence peak occurred between October 2017 and January 2018, and May 2018, respectively. Of 688 selected seedlings, mortality was 92.7% within one year. No seeds were observed in the SSB. Seedling height and leaf number positively affected seedling survival, while seed placement as measured by aspect also showed effects on survival. Conspecific and heterospecific density and herbivory did not show any clear effect. Higher probabilities of seedling survival were found in areas with larger canopy openness (≥12% canopy gap size) and in steeper microsites (≥35°). Synthesis. Masting is mainly studied as a population‐level phenomenon from the fruiting tree perspective. Our study of individual seedling fate revealed that intrinsic biotic factors and seed placement were key drivers of survival. Although biotic determinants such as competition from conspecifics or heterospecifics or herbivory did not determine survival, their ubiquitous presence may be an underlying equalizer in community dynamics where seedlings that overcome biotic pressures, if placed at the right microsite, are at better odds at being recruited to the next life history stages.
Concealed truth: Modeling reveals unique Quaternary distribution dynamics and refugia of four related endemic keystone Abies taxa on the Tibetan Plateau

Abstract Understanding the factors driving the Quaternary distribution of Abies in the Tibetan Plateau (TP) is crucial for biodiversity conservation and for predicting future anthropogenic impacts on ecosystems. Here, we collected Quaternary paleo‐, palynological, and phylogeographical records from across the TP and applied ecological niche models (ENMs) to obtain a profound understanding of the different adaptation strategies and distributional changes in Abies trees in this unique area. We identified environmental variables affecting the different historical biogeographies of four related endemic Abies taxa and rebuilt their distribution patterns over different time periods, starting from the late Pleistocene. In addition, modeling and phylogeographic results were used to predict suitable refugia for Abies forrestii, A. forrestii var. georgei, A. fargesii var. faxoniana, and A. recurvata. We supplemented the ENMs by investigating pollen records and diversity patterns of cpDNA for them. The overall reconstructed distributions of these Abies taxa were dramatically different when the late Pleistocene was compared with the present. All Abies taxa gradually receded from the south toward the north in the last glacial maximum (LGM). The outcomes showed two well‐differentiated distributions: A. fargesii var. faxoniana and A. recurvata occurred throughout the Longmen refuge, a temporary refuge for the LGM, while the other two Abies taxa were distributed throughout the Heqing refuge. Both the seasonality of precipitation and the mean temperature of the driest quarter played decisive roles in driving the distribution of A. fargesii var. faxoniana and A. recurvata, respectively; the annual temperature range was also a key variable that explained the distribution patterns of the other two Abies taxa. Different adaptation strategies of trees may thus explain the differing patterns of distribution over time at the TP revealed here for endemic Abies taxa.
Changes in Plasma Fatty Acids, Free Amino Acids, Antioxidant Defense, and Physiological Stress by Oleuropein Supplementation in Pigs Prior to Slaughter

Olive tree leaves are characterized for having not only a potent antioxidant power but also effects on glucose and lipid metabolism. The impact of the individual oleuropein (OLE), vitamin E + Se (VE), or a combined supplementation of oleuropein, vitamin E, and selenium (VEOLE) was evaluated on pig plasma metabolites under fasting prior to slaughter. VEOLE and OLE had lesser n-3 plasma polyunsaturated fatty acids and greater monounsaturated free fatty acids compared to control. The n-3-fatty acid mobilization was directly correlated with greater cystine and inversely with oxidized glutathione/reduced glutathione (GSSH/GSH) levels. This faster use of n-3 fatty acids might act as an indicator of glutathione synthesis mediated by an increase of cystine in plasma. Different correlations and linear adjustments were observed between plasma antioxidant power and free cystine, free glycine, free glutamine, monounsaturated free fatty acids, and total n-3. The best response to stress was found in VEOLE. Cortisol reached the greatest positive correlation with plasma total n-3 fatty acids, which suggests a faster uptake of n-3 for biological functions such as stress control or energy supply in the brain. From a practical point of view, an enhanced oxidative status as well as control of physiological stress prior to slaughter by the combined antioxidants supplementation might have positive effects on pork quality.
Preferential Coupling of Dopamine D2S and D2L Receptor Isoforms with Gi1 and Gi2 Proteins—In Silico Study

The dopamine D2 receptor belongs to rhodopsin-like G protein-coupled receptors (GPCRs) and it is an important molecular target for the treatment of many disorders, including schizophrenia and Parkinson’s disease. Here, computational methods were used to construct the full models of the dopamine D2 receptor short (D2S) and long (D2L) isoforms (differing with 29 amino acids insertion in the third intracellular loop, ICL3) and to study their coupling with Gi1 and Gi2 proteins. It was found that the D2L isoform preferentially couples with the Gi2 protein and D2S isoform with the Gi1 protein, which is in accordance with experimental data. Our findings give mechanistic insight into the interplay between isoforms of dopamine D2 receptors and Gi proteins subtypes, which is important to understand signaling by these receptors and their mediation by pharmaceuticals, in particular psychotic and antipsychotic agents.
Normal Pressure Hydrocephalus: Clinical Symptoms, Cerebrospinal Fluid Flow Metrics and White Matter Changes.

PURPOSE The aim of this study was to investigate correlations between clinical symptoms, cerebrospinal fluid flow metrics, hydrocephalus index, small-vessel disease, and white matter (WM) changes in normal pressure hydrocephalus (NPH). METHODS Aquaductal stroke volumes (ASVs), Z Evans index, Fazekas grading (FG), and diffusion tensor imaging measurements from WM bundles of 37 patients with NPH were retrospectively evaluated. Mann-Whitney U test between clinical symptoms and other variables and Spearman ρ correlations for relationships between variables and Kruskal-Wallis to correlate FG with nonclinical variables were used. RESULTS Patients with NPH had increased ASV (median 53 μL). No correlation was found between Z Evans index and ASV. Three groups of patients with dementia or ataxia or incontinence had increased ASV values than their counterparts without symptoms (55 vs 48.5 μL, 75 vs 47 μL, 64 vs 49.5 μL, respectively). Patients having 2 common symptoms of dementia and ataxia and patients having all 3 symptoms of dementia, ataxia, and incontinence were compared with ASV values of 63.5 versus 78 μL, respectively. Patients with FG 1 had median ASV values of 45 μL; FG 2, 82.5 μL; and FG 3, 59 μL. Patients with dementia had significantly higher apparent diffusion coefficient (ADC) values of corona radiata (CR) on both sides. There were no significant WM changes in patients with ataxia and incontinence. The Z Evans index was positively correlated with ADC values of CR on both sides and genu of corpus callosum. Fazekas grading was found positively correlated with ADC and negatively correlated with FA values of CR. CONCLUSIONS Patients with NPH, regardless of stages of the diseases, have increased ASV values and could benefit from shunting. Decreasing ASV values of patients with FG 3 comparing with those with FG 2 support the hypothesis of decreasing compliance of brain with aging and increasing severity of small-vessel disease.
Autophagy Function and Regulation in Kidney Disease

Autophagy is a dynamic process by which intracellular damaged macromolecules and organelles are degraded and recycled for the synthesis of new cellular components. Basal autophagy in the kidney acts as a quality control system and is vital for cellular metabolic and organelle homeostasis. Under pathological conditions, autophagy facilitates cellular adaptation; however, activation of autophagy in response to renal injury may be insufficient to provide protection, especially under dysregulated conditions. Kidney-specific deletion of Atg genes in mice has consistently demonstrated worsened acute kidney injury (AKI) outcomes supporting the notion of a pro-survival role of autophagy. Recent studies have also begun to unfold the role of autophagy in progressive renal disease and subsequent fibrosis. Autophagy also influences tubular cell death in renal injury. In this review, we reported the current understanding of autophagy regulation and its role in the pathogenesis of renal injury. In particular, the classic mammalian target of rapamycin (mTOR)-dependent signaling pathway and other mTOR-independent alternative signaling pathways of autophagy regulation were described. Finally, we summarized the impact of autophagy activation on different forms of cell death, including apoptosis and regulated necrosis, associated with the pathophysiology of renal injury. Understanding the regulatory mechanisms of autophagy would identify important targets for therapeutic approaches.
Duodenal Ulceration in a Child with Coeliac Disease

Coeliac disease (CD) is a gluten-dependent inflammatory disease of the small bowel that affects up to 1% of the global population. Herein, the presence of ulcers, erosions, or strictures in the duodenum for non-advanced cases of CD is a rarity. Case report: We present a clinical case of a 17-year-old girl, who from the age of 9, had suffered from erosive Helicobacter pylori (HP)-associated gastritis and erosive duodenitis. At 16, she was diagnosed with a duodenal ulcer, complicated by cicatricial deformity of the bulb. While an atypical course in the development of the disease had led to the initial delay in diagnosis, a serum study and an intestinal biopsy confirmed CD. Discussion: A recent study found an elevated rate of peptic ulcer disease in patients with CD. From literature searches, comorbid HP infection and CD have indeed been widely reported, whereas cases highlighting the prevalence of CD-associated peptic ulcers have been observed and reported in only a few instances. Consequently, greater awareness is warranted and must be exercised for identifying the origins of ulcerative lesions that may be CD-related or -derived.
Osteochondritis dissecans of the talus: case report on

SUMMARY Historically the investigators studying the etiology of osteochondritis dissecans can be grouped into two schools: (a) those considering trauma to previously normal bone as the chief cause; and (b) those noting causes other than trauma as being the primary reason for the lesion's development. In the case studies presented here, three medial lesions in two siblings are discussed. In neither case could trauma be substantiated.
Methods for Reducing the Toxicity of Metal and Metal Oxide NPs as Biomedicine

The rapid development of medicine has forced equally rapid progress in the field of pharmaceuticals. In connection with the expensive and time-consuming process of finding new drugs, great emphasis is put on the design and use of metal and metal oxides nanoparticles in nanomedicine. The main focus is on comprehensive presentation of both physicochemical properties and the possibilities of using, in particular, silver (Ag) and gold (Au) nanoparticles, as well as zinc oxide (ZnO) and titanium oxide (TiO2) nanoparticles as drug carriers and in the treatment of cancer. An important element of this subject is the possibility of occurrence of toxic effects of these nanoparticles. For this reason, possible mechanisms of toxic actions are presented, as well as methods used to reduce their toxicity to ensure the safety of drug carriers based on these nanostructures.
Empirical Failures of the Claim That Autistic People Lack a Theory of Mind

The claim that autistic people lack a theory of mind—that they fail to understand that other people have a mind or that they themselves have a mind—pervades psychology. This article (a) reviews empirical evidence that fails to support the claim that autistic people are uniquely impaired, much less that all autistic people are universally impaired, on theory-of-mind tasks; (b) highlights original findings that have failed to replicate; (c) documents multiple instances in which the various theory-of-mind tasks fail to relate to each other and fail to account for autistic traits, social interaction, and empathy; (c) summarizes a large body of data, collected by researchers working outside the theory-of-mind rubric, that fails to support assertions made by researchers working inside the theory-of-mind rubric; and (d) concludes that the claim that autistic people lack a theory of mind is empirically questionable and societally harmful.
The Immunomodulary Effects of Systematic Exercise in Older Adults and People with Parkinson’s Disease

We sought to investigate whether regular balance training of moderate intensity (BT) has an effect on changes in selected cytokines, neurotrophic factors, CD200 and fractalkine in healthy older adults and participants with Parkinson’s disease (PD). Sixty-two subjects were divided into groups depending on experimental intervention: (1) group of people with PD participating in BT (PDBT), (2) group of healthy older people participating in BT (HBT), (3,4) control groups including healthy individuals (HNT) and people with PD (PDNT). Blood samples were collected twice: before and after 12 weeks of balance exercise (PDBT, HBT), or 12 weeks apart (PDNT, HNT). The study revealed significant increase of interleukin10 (PDBT, p = 0.026; HBT, p = 0.011), β-nerve growth factor (HBT, p = 0.002; PDBT, p = 0.016), transforming growth factor-β1 (PDBT, p = 0.018; HBT, p < 0.004), brain-derived neurotrophic factor (PDBT, p = 0.011; HBT, p < 0.001) and fractalkine (PDBT, p = 0.045; HBT, p < 0.003) concentration only in training groups. In PDBT, we have found a significant decrease of tumor necrosis factor alpha. No training effect on concentration of interleukin6, insulin-like growth factor 1 and CD200 was observed in both training and control groups. Regular training can modulate level of inflammatory markers and induce neuroprotective mechanism to reduce the inflammatory response.
The dynamics of shapes of vesicle membranes with time dependent spontaneous curvature

We study the time evolution of the shape of a vesicle membrane under time-dependent spontaneous curvature by means of phase-field model. We introduce the variation in time of the spontaneous curvature via a second field which represents the concentration of a substance that anchors with the lipid bilayer thus changing the local curvature and producing constriction. This constriction is mediated by the action on the membrane of an structure resembling the role of a Z ring. Our phase-field model is able to reproduce a number of different shapes that have been experimentally observed. Different shapes are associated with different constraints imposed upon the model regarding conservation of membrane area. In particular, we show that if area is conserved our model reproduces the so-called L-form shape. By contrast, if the area of the membrane is allowed to grow, our model reproduces the formation of a septum in the vicinity of the constriction. Furthermore, we propose a new term in the free energy which allows the membrane to evolve towards eventual pinching.
An Analytical Conductance Model for Gas Detection Based on a Zigzag Carbon Nanotube Sensor

Recent advances in nanotechnology have revealed the superiority of nanocarbon species such as carbon nanotubes over other conventional materials for gas sensing applications. In this work, analytical modeling of the semiconducting zigzag carbon nanotube field-effect transistor (ZCNT-FET) based sensor for the detection of gas molecules is demonstrated. We propose new analytical models to strongly simulate and investigate the physical and electrical behavior of the ZCNT sensor in the presence of various gas molecules (CO2, H2O, and CH4). Therefore, we start with the modeling of the energy band structure by acquiring the new energy dispersion relation for the ZCNT and introducing the gas adsorption effects to the band structure model. Then, the electrical conductance of the ZCNT is modeled and formulated while the gas adsorption effect is considered in the conductance model. The band structure analysis indicates that, the semiconducting ZCNT experiences band gap variation after the adsorption of the gases. Furthermore, the bandgap variation influences the conductance of the ZCNT and the results exhibit increments of the ZCNT conductance in the presence of target gases while the minimum conductance shifted upward around the neutrality point. Besides, the I-V characteristics of the sensor are extracted from the conductance model and its variations after adsorption of different gas molecules are monitored and investigated. To verify the accuracy of the proposed models, the conductance model is compared with previous experimental and modeling data and a good consensus is observed. It can be concluded that the proposed analytical models can successfully be applied to predict sensor behavior against different gas molecules.
VAPB ER-Aggregates, A Possible New Biomarker in ALS Pathology

A point mutation (P56S) in the gene-encoding vesicle-associated membrane-protein-associated protein B (VAPB) leads to an autosomal-dominant form of amyotrophic lateral sclerosis (ALS), classified as ALS-8. The mutant VAPB is characterized by ER-associated aggregates that lead to a complete reorganization of ER structures. Growing evidences suggest VAPB involvement in ALS pathomechanisms. In fact, numerous studies demonstrated VAPB alteration also in sporadic ALS (sALS) and showed the presence of its aggregates when others ALS-related gene are mutant. Recently, the identification of new biomarkers in peripheral blood mononuclear cells (PBMCs) has been proposed as a good noninvasive option for studying ALS. Here, we evaluated VAPB as a possible ALS pathologic marker analyzing PBMCs of sALS patients. Immunofluorescence analysis (IFA) showed a peculiar pattern of VAPB aggregates in sALS, not evident in healthy control (HC) subjects and in Parkinson’s disease (PD) PBMCs. This specific pattern led us to suppose that VAPB could be misfolded in sALS. The data indirectly confirmed by flow cytometry assay (FCA) showed a reduction of VAPB fluorescent signals in sALS. However, our observations were not associated with the presence of a genetic mutation or altered gene expression of VAPB. Our study brings further evidences of the VAPB role in ALS as a diagnostic biomarker.
Cell Cycle and DNA Repair Regulation in the Damage Response: Protein Phosphatases Take Over the Reins

Cells are constantly suffering genotoxic stresses that affect the integrity of our genetic material. Genotoxic insults must be repaired to avoid the loss or inappropriate transmission of the genetic information, a situation that could lead to the appearance of developmental abnormalities and tumorigenesis. To combat this threat, eukaryotic cells have evolved a set of sophisticated molecular mechanisms that are collectively known as the DNA damage response (DDR). This surveillance system controls several aspects of the cellular response, including the detection of lesions, a temporary cell cycle arrest, and the repair of the broken DNA. While the regulation of the DDR by numerous kinases has been well documented over the last decade, the complex roles of protein dephosphorylation have only recently begun to be investigated. Here, we review recent progress in the characterization of DDR-related protein phosphatases during the response to a DNA lesion, focusing mainly on their ability to modulate the DNA damage checkpoint and the repair of the damaged DNA. We also discuss their protein composition and structure, target specificity, and biochemical regulation along the different stages encompassed in the DDR. The compilation of this information will allow us to better comprehend the physiological significance of protein dephosphorylation in the maintenance of genome integrity and cell viability in response to genotoxic stress.
Nomogram based on clinical characteristics for preoperative prediction of perineural invasion in gastric cancer

Purpose Gastric cancer (GC) has a poor prognosis and high rate of recurrence. Perineural invasion (PNI) is a prognostic factor in GC that is associated with a high risk of systemic recurrence. Preoperative identification of PNI may facilitate patient stratification and optimal preoperative treatment. We therefore developed and validated a nomogram for the preoperative prediction of PNI. Methods We retrospectively collected clinical data from 261 GC patients, who were randomly assigned to training (n = 185) and validation (n = 76) sets. The least absolute shrinkage and selection operator regression model was used to identify potentially relevant clinical parameters, and multivariable logistic regression analysis was used to develop the nomogram. Results The nomogram consisted of body mass index, immunoglobulin A level, and computed tomography-based T- and N-stages. Good calibration was observed for both the training and validation sets, with areas under the curve of 0.77 and 0.79, respectively. Decision curve analysis revealed that the nomogram was clinically relevant. Conclusion We developed and validated a nomogram for the preoperative prediction of PNI in patients with GC. Our nomogram may facilitate the identification of high-risk patients and optimization of preoperative decision-making.