bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental genetics of color pattern establishment in cats
Authors: Kaelin Christopher B. , McGowan Kelly A. , Barsh Gregory S. 
Published: September 2021

AbstractIntricate color patterns are a defining aspect of morphological diversity in the Felidae. We applied morphological and single-cell gene expression analysis to fetal skin of domestic cats to identify when, where, and how, during fetal development, felid color patterns are established. Early in development, we identify stripe-like alterations in epidermal thickness preceded by a gene expression pre-pattern. The secreted Wnt inhibitor encoded by Dickkopf 4 plays a central role in this process, and is mutated in cats with the Ticked pattern type. Our results bring molecular understanding to how the leopard got its spots, suggest that similar mechanisms underlie periodic color pattern and periodic hair follicle spacing, and identify targets for diverse pattern variation in other mammals.
Adoptive immunotherapy with transient anti-CD4 treatment enhances anti-tumor response by increasing IL-18Rαhi CD8+ T cells
Authors: Kim Seon-Hee , Cho Eunjung , Kim Yu I. , Han Chungyong , Choi Beom K. , Kwon Byoung S. 
Published: September 2021

AbstractAdoptive T cell therapy (ACT) requires lymphodepletion preconditioning to eliminate immune-suppressive elements and enable efficient engraftment of adoptively transferred tumor-reactive T cells. As anti-CD4 monoclonal antibody depletes CD4+ immune-suppressive cells, the combination of anti-CD4 treatment and ACT has synergistic potential in cancer therapy. Here, we demonstrate a post-ACT conditioning regimen that involves transient anti-CD4 treatment (CD4post). Using murine melanoma, the combined effect of cyclophosphamide preconditioning (CTXpre), CD4post, and ex vivo primed tumor-reactive CD8+ T-cell infusion is presented. CTXpre/CD4post increases tumor suppression and host survival by accelerating the proliferation and differentiation of ex vivo primed CD8+ T cells and endogenous CD8+ T cells. Endogenous CD8+ T cells enhance effector profile and tumor-reactivity, indicating skewing of the TCR repertoire. Notably, enrichment of polyfunctional IL-18Rαhi CD8+ T cell subset is the key event in CTXpre/CD4post-induced tumor suppression. Mechanistically, the anti-tumor effect of IL-18Rαhi subset is mediated by IL-18 signaling and TCR–MHC I interaction. This study highlights the clinical relevance of CD4post in ACT and provides insights regarding the immunological nature of anti-CD4 treatment, which enhances anti-tumor response of CD8+ T cells.
In situ inorganic conductive network formation in high-voltage single-crystal Ni-rich cathodes
Authors: Fan Xinming , Ou Xing , Zhao Wengao , Liu Yun , Zhang Bao , Zhang Jiafeng , Zou Lianfeng , Seidl Lukas , Li Yangzhong , Hu Guorong , Battaglia Corsin , Yang Yong 
Published: September 2021

AbstractHigh nickel content in LiNixCoyMnzO2 (NCM, x ≥ 0.8, x + y + z = 1) layered cathode material allows high specific energy density in lithium-ion batteries (LIBs). However, Ni-rich NCM cathodes suffer from performance degradation, mechanical and structural instability upon prolonged cell cycling. Although the use of single-crystal Ni-rich NCM can mitigate these drawbacks, the ion-diffusion in large single-crystal particles hamper its rate capability. Herein, we report a strategy to construct an in situ Li1.4Y0.4Ti1.6(PO4)3 (LYTP) ion/electron conductive network which interconnects single-crystal LiNi0.88Co0.09Mn0.03O2 (SC-NCM88) particles. The LYTP network facilitates the lithium-ion transport between SC-NCM88 particles, mitigates mechanical instability and prevents detrimental crystalline phase transformation. When used in combination with a Li metal anode, the LYTP-containing SC-NCM88-based cathode enables a coin cell capacity of 130 mAh g−1 after 500 cycles at 5 C rate in the 2.75-4.4 V range at 25 °C. Tests in Li-ion pouch cell configuration (i.e., graphite used as negative electrode active material) demonstrate capacity retention of 85% after 1000 cycles at 0.5 C in the 2.75-4.4 V range at 25 °C for the LYTP-containing SC-NCM88-based positive electrode.
Global relationships between crop diversity and nutritional stability
Authors: Nicholson Charlie C. , Emery Benjamin F. , Niles Meredith T. 
Published: September 2021

AbstractNutritional stability – a food system’s capacity to provide sufficient nutrients despite disturbance – is an important, yet challenging to measure outcome of diversified agriculture. Using 55 years of data across 184 countries, we assemble 22,000 bipartite crop-nutrient networks to quantify nutritional stability by simulating crop and nutrient loss in a country, and assess its relationship to crop diversity across regions, over time and between imports versus in country production. We find a positive, saturating relationship between crop diversity and nutritional stability across countries, but also show that over time nutritional stability remained stagnant or decreased in all regions except Asia. These results are attributable to diminishing returns on crop diversity, with recent gains in crop diversity among crops with fewer nutrients, or with nutrients already in a country’s food system. Finally, imports are positively associated with crop diversity and nutritional stability, indicating that many countries’ nutritional stability is market exposed.
Transcriptional network involving ERG and AR orchestrates Distal-less homeobox-1 mediated prostate cancer progression
Authors: Goel Sakshi , Bhatia Vipul , Kundu Sushmita , Biswas Tanay , Carskadon Shannon , Gupta Nilesh , Asim Mohammad , Morrissey Colm , Palanisamy Nallasivam , Ateeq Bushra 
Published: September 2021

AbstractDistal-less homeobox-1 (DLX1) is a well-established non-invasive biomarker for prostate cancer (PCa) diagnosis, however, its mechanistic underpinnings in disease pathobiology are not known. Here, we reveal the oncogenic role of DLX1 and show that abrogating its function leads to reduced tumorigenesis and metastases. We observed that ~60% of advanced-stage and metastatic patients display higherDLX1levels. Moreover, ~96% ofTMPRSS2-ERGfusion-positive and ~70% of androgen receptor (AR)-positive patients show elevatedDLX1, associated with aggressive disease and poor survival. Mechanistically, ERG coordinates with enhancer-bound AR and FOXA1 to drive transcriptional upregulation ofDLX1in ERG-positive background. However, in ERG-negative context, AR/AR-V7 and FOXA1 suffice to upregulateDLX1. Notably, inhibiting ERG/AR-mediatedDLX1transcription using BET inhibitor (BETi) or/and anti-androgen drugs reduce its expression and downstream oncogenic effects. Conclusively, this study establishesDLX1as a direct-target of ERG/AR with an oncogenic role and demonstrates the clinical significance of BETi and anti-androgens for DLX1-positive patients.
Gene interfered-ferroptosis therapy for cancers
Authors: Gao Jinliang , Luo Tao , Wang Jinke 
Published: September 2021

AbstractAlthough some effective therapies have been available for cancer, it still poses a great threat to human health and life due to its drug resistance and low response in patients. Here, we develop a ferroptosis-based therapy by combining iron nanoparticles and cancer-specific gene interference. The expression of two iron metabolic genes (FPNandLCN2) was selectively knocked down in cancer cells by Cas13a or microRNA controlled by a NF-κB-specific promoter. Cells were simultaneously treated by iron nanoparticles. As a result, a significant ferroptosis was induced in a wide variety of cancer cells. However, the same treatment had little effect on normal cells. By transferring genes with adeno-associated virus and iron nanoparticles, the significant tumor growth inhibition and durable cure were obtained in mice with the therapy. In this work, we thus show a cancer therapy based on gene interference-enhanced ferroptosis.
A compendium of uniformly processed human gene expression and splicing quantitative trait loci
Authors: Kerimov Nurlan , Hayhurst James D. , Peikova Kateryna , Manning Jonathan R. , Walter Peter , Kolberg Liis , Samoviča Marija , Sakthivel Manoj Pandian , Kuzmin Ivan , Trevanion Stephen J. , Burdett Tony , Jupp Simon , Parkinson Helen , Papatheodorou Irene , Yates Andrew D. , Zerbino Daniel R. , Alasoo Kaur 
Published: September 2021

AbstractMany gene expression quantitative trait locus (eQTL) studies have published their summary statistics, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and co-localization. However, technical differences between these datasets are a barrier to their widespread use. Consequently, target genes for most genome-wide association study (GWAS) signals have still not been identified. In the present study, we present the eQTL Catalogue (https://www.ebi.ac.uk/eqtl), a resource of quality-controlled, uniformly re-computed gene expression and splicing QTLs from 21 studies. We find that, for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies. Although most QTLs were shared between most bulk tissues, we identified a greater diversity of cell-type-specific QTLs from purified cell types, a subset of which also manifested as new disease co-localizations. Our summary statistics are freely available to enable the systematic interpretation of human GWAS associations across many cell types and tissues.
Lateral resolution limit of laser Doppler vibrometer microscopes for the measurement of surface acoustic waves
Authors: Kowarsch Robert , Rembe Christian 
Published: September 2021

AbstractThe lateral or transverse resolution of single-point interferometers for vibration measurement is especially critical for microelectromechanical systems (MEMS) vibrating up to the gigahertz range. In this regime, the acoustic wavelengths are typically in the range of the size of the laser focus. Thus, a successful vibration measurement requires distinct knowledge about the lateral resolution limit and its dependencies with instrumentation parameters. In this paper, we derive an analytic approximation formula, which allows for estimation of the systematic measurement deviation of the vibration amplitude and, thus, a definition of the lateral resolution limit of single-point interferometers for vibration measurement. Further, a compensation and an optimum numerical aperture are proposed the reduce the measurement deviation. For this, the model includes a laser-interferometer microscope of Mach-Zehnder type with Gaussian laser beams considering the Gouy effect and wavefront curvature. As a measurement scenario, an unidirectional surface acoustic wave (SAW) is regarded. The theoretic findings have been validated in the experiment with a representative vibration measurement on a SAW filter at $$433\,{\mathrm {MHz}}$$433MHzwith our heterodyne laser-Doppler interferometer with offset-locked semiconductor lasers. The provided formulas help instrument designers and users to choose suitable instrument parameters, especially the numerical aperture of the utilized microscope objective.
Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family
Authors: Emelianova Katie , Martínez Martínez Andrea , Campos-Dominguez Lucia , Kidner Catherine 
Published: September 2021

AbstractBegonia is an important horticultural plant group, as well as one of the most speciose Angiosperm genera, with over 2000 described species. Genus wide studies of genome size have shown that Begonia has a highly variable genome size, and analysis of paralog pairs has previously suggested that Begonia underwent a whole genome duplication. We address the contribution of gene duplication to the generation of diversity in Begonia using a multi-tissue RNA-seq approach. We chose to focus on chalcone synthase (CHS), a gene family having been shown to be involved in biotic and abiotic stress responses in other plant species, in particular its importance in maximising the use of variable light levels in tropical plants. We used RNA-seq to sample six tissues across two closely related but ecologically and morphologically divergent species, Begonia conchifolia and B. plebeja, yielding 17,012 and 19,969 annotated unigenes respectively. We identified the chalcone synthase gene family members in our Begonia study species, as well as in Hillebrandia sandwicensis, the monotypic sister genus to Begonia, Cucumis sativus, Arabidopsis thaliana, and Zea mays. Phylogenetic analysis suggested the CHS gene family has high duplicate turnover, all members of CHS identified in Begonia arising recently, after the divergence of Begonia and Cucumis. Expression profiles were similar within orthologous pairs, but we saw high inter-ortholog expression variation. Sequence analysis showed relaxed selective constraints on some ortholog pairs, with substitutions at conserved sites. Evidence of pseudogenisation and species specific duplication indicate that lineage specific differences are already beginning to accumulate since the divergence of our study species. We conclude that there is evidence for a role of gene duplication in generating diversity through sequence and expression divergence in Begonia.
Uric acid as a prognostic factor and critical marker of COVID-19
Authors: Li Gang , Wu Xia , Zhou Chen-liang , Wang Ye-ming , Song Bin , Cheng Xiao-bin , Dong Qiu-fen , Wang Liu-lin , You Sha-sha , Ba Yuan-ming 
Published: September 2021

AbstractThe purpose of this study is to explore whether uric acid (UA) can independently act as a prognostic factor and critical marker of the 2019 novel corona virus disease (COVID-19). A multicenter, retrospective, and observational study including 540 patients with confirmed COVID-19 was carried out at four designated hospitals in Wuhan. Demographic, clinical, laboratory data were collected and analyzed. The primary end point was in-hospital death of patients with COVID-19. The concentration of admission UA (adUA) and the lowest concentration of uric acid during hospitalization (lowUA) in the dead patients were significantly lower than those in the survivors. Multivariate logistic regression analysis showed the concentration of lowUA (OR 0.986, 95% CI 0.980–0.992, p < 0.001) was able to independently predict the risk of in-hospital death. The mean survival time in the low-level group of lowUA was significantly lower than other groups. When lowUA was ≤ 166 µmol/L, the sensitivity and specificity in predicting hospital short-term mortality were 76.9%, (95% CI 68.5–85.1%) and 74.9% (95% CI 70.3–78.9%). This retrospective study determined that the lowest concentration of UA during hospitalization can be used as a prognostic indicator and a marker of disease severity in severe patients with COVID-19.
Π-GISANS: probing lateral structures with a fan shaped beam
Authors: Vorobiev Alexei , Paracini Nicolò , Cárdenas Marité , Wolff Max 
Published: September 2021

AbstractWe have performed grazing incidence neutron small angle scattering using a fan shaped incident beam focused along one dimension. This allows significantly reduced counting times for measurements of lateral correlations parallel to an interface or in a thin film where limited depth resolution is required. We resolve the structure factor of iron inclusions in aluminium oxide and show that the ordering of silica particles deposited on a silicon substrate depends on their size. We report hexagonal packing for 50 nm but not for 200 nm silica spheres deposited by a modified Langmuir-Schaefer method on a silicon substrate. For the 200 nm particles we extract the particles shape from the form factor. Moreover, we report dense packing of the particles spread on a free water surface. We name this method π-GISANS to highlight that it differs from GISANS as it gives lateral information while averaging the in-depth structure.
A sex-specific propensity-adjusted analysis of colonic adenoma detection rates in a screening cohort
Authors: Wernly Sarah , Wernly Bernhard , Semmler Georg , Bachmayer Sebastian , Niederseer David , Stickel Felix , Huber-Schönauer Ursula , Aigner Elmar , Datz Christian 
Published: September 2021

AbstractThe prevalence of colorectal adenoma and advanced adenoma (AA) differs between sexes. Also, the optimal age for the first screening colonoscopy is under debate. We, therefore, performed a sex-specific and age-adjusted comparison of adenoma, AA and advanced neoplasia (AN) rates in a real-world screening cohort. In total, 2824 asymptomatic participants between 45- and 60-years undergoing screening colonoscopy at a single-centre in Austria were evaluated. 46% were females and mean age was 53 ± 4 years. A propensity score for being female was calculated, and adenoma, AA and AN detection rates evaluated using uni- and multivariable logistic regression. Sensitivity analyses for three age groups (group 1: 45 to 49 years, n = 521, 41% females, mean age 47 ± 1 years; group 2: 50 to 54 years, n = 1164, 47% females, mean age 52 ± 1 years; group 3: 55 to 60 years, n = 1139, 46% females, mean age 57 ± 2 years) were performed. The prevalence of any adenoma was lower in females (17% vs. 30%; OR 0.46, 95% CI 0.38–0.55; p < 0.001) and remained so after propensity score adjustment for baseline characteristics and lifestyle factors (aOR 0.52, 95% CI 0.41–0.66; p < 0.001). The same trend was seen for AA with a significantly lower prevalence in females (3% vs. 7%; OR 0.38, 95% CI 0.26–0.55; p < 0.001) that persisted after propensity score adjustment (aOR 0.54, 95% CI 0.34–0.86; p = 0.01). Also, all age-group sensitivity analyses showed lower adenoma, AA and AN rates in females. Similar numbers needed to screen to detect an adenoma, an AA or AN were found in female age group 3 and male age group 1. Colorectal adenoma, AA and AN were consistently lower in females even after propensity score adjustment and in all age-adjusted sensitivity analyses. Our study may add to the discussion of the optimal age for initial screening colonoscopy which may differ between the sexes.
Tianeptine modulates synaptic vesicle dynamics and favors synaptic mitochondria processes in socially isolated rats
Authors: Perić Ivana , Costina Victor , Djordjević Snežana , Gass Peter , Findeisen Peter , Inta Dragoš , Borgwardt Stefan , Filipović Dragana 
Published: September 2021

AbstractDeregulation of synaptic function and neurotransmission has been linked with the development of major depression disorder (MDD). Tianeptine (Tian) has been used as antidepressant with anxiolytic properties and recently as a nootropic to improve cognitive performance, but its mechanism of action is unknown. We conducted a proteomic study on the hippocampal synaptosomal fractions of adult male Wistar rats exposed to chronic social isolation (CSIS, 6 weeks), an animal model of depression and after chronic Tian treatment in controls (nootropic effect) and CSIS-exposed rats (lasting 3 weeks of 6-week CSIS) (therapeutic effect). Increased expression of Syn1 and Camk2-related neurotransmission, vesicle transport and energy processes in Tian-treated controls were found. CSIS led to upregulation of proteins associated with actin cytoskeleton, signaling transduction and glucose metabolism. In CSIS rats, Tian up-regulated proteins involved in mitochondrial energy production, mitochondrial transport and dynamics, antioxidative defense and glutamate clearance, while attenuating the CSIS-increased glycolytic pathway and cytoskeleton organization proteins expression and decreased the expression of proteins involved in V-ATPase and vesicle endocytosis. Our overall findings revealed that synaptic vesicle dynamics, specifically exocytosis, and mitochondria-related energy processes might be key biological pathways modulated by the effective nootropic and antidepressant treatment with Tian and be a potential target for therapeutic efficacy of the stress-related mood disorders.
The complex evolution of the metazoan HSP70 gene family
Authors: Yu Er-meng , Yoshinaga Tatsuki , Jalufka Frank L. , Ehsan Hashimul , Mark Welch David B. , Kaneko Gen 
Published: September 2021

AbstractThe metazoan 70-kDa heat shock protein (HSP70) family contains several members localized in different subcellular compartments. The cytosolic members have been classified into inducible HSP70s and constitutive heat shock cognates (HSC70s), but their distinction and evolutionary relationship remain unclear because of occasional reports of “constitutive HSP70s” and the lack of cross-phylum comparisons. Here we provide novel insights into the evolution of these important molecular chaperones. Phylogenetic analyses of 125 full-length HSP70s from a broad range of phyla revealed an ancient duplication that gave rise to two lineages from which all metazoan cytosolic HSP70s descend. One lineage (A) contains a relatively small number of genes from many invertebrate phyla, none of which have been shown to be constitutively expressed (i.e., either inducible or unknown). The other lineage (B) included both inducible and constitutive genes from diverse phyla. Species-specific duplications are present in both lineages, and Lineage B contains well-supported phylum-specific clades for Platyhelminthes, Rotifera, Nematoda, Porifera/Cnidaria, and Chordata. Some genes in Lineage B have likely independently acquired inducibility, which may explain the sporadic distribution of “HSP70” or “HSC70” in previous phylogenetic analyses. Consistent with the diversification history within each group, inducible members show lower purifying selection pressure compared to constitutive members. These results illustrate the evolutionary history of the HSP70 family, encouraging us to propose a new nomenclature: “HSP70 + subcellular localization + linage + copy number in the organism + inducible or constitutive, if known.” e.g., HSP70cA1i for cytosolic Lineage A, copy 1, inducible.
Evaporation and deposition of inclined colloidal droplets
Authors: Kim Jin Young , Gonçalves Marta , Jung Narina , Kim Hyoungsoo , Weon Byung Mook 
Published: September 2021

AbstractColloidal droplets on flat solid substrates commonly leave symmetric ring-like deposits due to coffee-ring flows during evaporation. On inclined substrates, droplet shapes may become asymmetric by gravity. On this basis, it is not clear how their evaporation dynamics and final deposits are changed depending on inclination. Here we explore evaporation and deposition dynamics of colloidal droplets on inclined substrates, mainly by controlling colloidal particle size, substrate inclination, and relative humidity, which are crucial to gravitational intervention and evaporation dynamics. We experimentally investigate two different flows with opposite directions: downward sedimentation flows by gravity ($$v_s$$

v
s

) and upward capillary flows by evaporation ($$v_c$$

v
c

). We find that the competition of two flows determines the formation of final deposits with a flow speed ratio of $$\alpha = v_s/v_c$$

α
=

v
s

/

v
c

. Notably, for $$\alpha$$
α
$$\ll$$
≪
1, evaporation-driven upward flows overwhelm sedimentation-driven downward flows, resulting in accentuated particle movement towards the top ring, which seems to defy gravitational intervention. We suggest a possible explanation for the flow speed dependence of final deposits in evaporating colloidal droplets. This study offers a framework to understand the intervention of inclination to the formation of final deposits and how to overcome the deposit pattern radial asymmetry, achieving symmetric deposit widths from inclined colloidal droplets.