Miracle-dz/UniFAR-FTUs huggingface dataset:
The Tomato DELLA Protein PROCERA Promotes Abscisic Acid Responses in Guard Cells by Upregulating an Abscisic Acid Transporter1

The tomato DELLA protein PROCERA promotes abscisic acid-induced stomatal closure and gene expression by upregulating expression of the ABA transporter ABA-IMPORTING TRANSPORTER1 in guard cells. Plants reduce transpiration through stomatal closure to avoid drought stress. While abscisic acid (ABA) has a central role in the regulation of stomatal closure under water-deficit conditions, we demonstrated in tomato (Solanum lycopersicum) that a gibberellin response inhibitor, the DELLA protein PROCERA (PRO), promotes ABA-induced stomatal closure and gene transcription in guard cells. To study how PRO affects stomatal closure, we performed RNA-sequencing analysis of isolated guard cells and identified the ABA transporters ABA-IMPORTING TRANSPORTER1.1 (AIT1.1) and AIT1.2, also called NITRATE TRANSPORTER1/PTR TRANSPORTER FAMILY4.6 in Arabidopsis (Arabidopsis thaliana), as being upregulated by PRO. Tomato has four AIT1 genes, but only AIT1.1 and AIT1.2 were upregulated by PRO, and only AIT1.1 exhibited high expression in guard cells. Functional analysis of AIT1.1 in yeast (Saccharomyces cerevisiae) confirmed its activity as an ABA transporter, possibly an importer. A clustered regularly interspaced short palindromic repeats-Cas9–derived ait1.1 mutant exhibited an increased transpiration, a larger stomatal aperture, and a reduced stomatal response to ABA. Moreover, ait1.1 suppressed the promoting effects of PRO on ABA-induced stomatal closure and gene expression in guard cells, suggesting that the effects of PRO on stomatal aperture and transpiration are AIT1.1-dependent. Previous studies suggest a negative crosstalk between gibberellin and ABA that is mediated by changes in hormone biosynthesis and signaling. The results of this study suggest this crosstalk is also mediated by changes in hormone transport.
Immunohistochemical Localization of the Cytoskeletal Proteins in the Testes of the Lesser Mouse Deer (Tragulus javanicus)

Abstract. This study demonstrated the immunohistochemical localization of cytoskeletal proteins, cytokeratin, desmin, vimentin, &agr;-tubulin and &agr;-smooth muscle actin (&agr;-SMA) in the testes of adult and immature lesser mouse deer (Tragulus javanicus). Desmin was found in the sub-epithelial myoid cells of epididymal ducts. The immunoreactivity for vimentin was shown in the peritubular myoid cells and around the nuclei of the Sertoli cells of which the positions indicated various arrangements. In the Sertoli cells, vimentin filaments between the basement membrane and the nucleus were elongated with the migration of the nucleus toward the upper part. Furthermore, vimentin was detected in the Leydig cells and the sub-epithelial myoid cells of epididymal ducts. Alpha-tubulin was apparently extended to the tip of each Sertoli cell cytoplasm, and &agr;-SMA was found in the peritubular myoid cells and the sub-epithelial myoid cells of epididymal ducts. On the other hand, cytokeratin and desmin were not detected in the Sertoli cells, Leydig cells, spermatogenic cells and peritubular myoid cells. In the mouse deer testes, vimentin filaments of the Sertoli cells may not be involved in the migration of the elongated spermatids and spermiation like as rat Sertoli cells because the supranuclear extension of vimentin was scanty.
Ant Species Identity has a Greater Effect than Fire on the Outcome of an Ant Protection System in Brazilian Cerrado

Although fire‐ and ant–plant interactions influence the community structure and dynamics of Neotropical savannas, no previous studies have considered their simultaneous effects on target host plants. We monitored the effect of ant exclusion for 3 years on leaf area loss to leaf chewing insects, thrips abundance, and reproductive output of the extrafloral nectary‐bearing shrub, Peixotoa tomentosa (Malpighiaceae). We predicted that the impact of ants on herbivores and plants would depend on the ant species, and that fire would reduce the effect of ants. We deliberately chose control plants that differed in their occupant ant species. Fire occurred in the second year of the study, allowing us to determine its effect on the benefit afforded by ants. Ants reduced leaf area loss and thrips abundance, and increased fruit and seed production in all 3 years. Some ant species were more effective than others, while plants with multiple ant species suffered higher leaf area loss than plants with a single ant species. In the year following the fire, leaf damage was greater than in the other years, regardless of the ant species, and the proportional effect of ants in reducing damage was less. Interactions affecting thrips abundance did not change following fire, nor was the benefit to the plant proportionally reduced. Overall, the identity of the ant species had a greater effect than did the occurrence of fire on the ant–herbivore–plant interaction: the identity of the ant species influenced leaf area loss, thrips numbers, and bud and seed production, while fire only modified the impact of ants on the amount of leaf area consumed by insect herbivores.
Endothelial protective factors BMP9 and BMP10 inhibit CCL2 release by human vascular endothelial cells

ABSTRACT Bone morphogenetic protein 9 (BMP9) and BMP10 are circulating ligands that mediate endothelial cell (EC) protection via complexes of the type I receptor ALK1 and the type II receptors activin type-IIA receptor (ACTR-IIA) and bone morphogenetic type II receptor (BMPR-II). We previously demonstrated that BMP9 induces the expression of interleukin-6, interleukin-8 and E-selectin in ECs and might influence their interactions with monocytes and neutrophils. We asked whether BMP9 and BMP10 regulate the expression of chemokine (C-C motif) ligand 2 (CCL2), a key chemokine involved in monocyte–macrophage chemoattraction. Here, we show that BMP9 and BMP10 repress basal CCL2 expression and release from human pulmonary artery ECs and aortic ECs. The repression was dependent on ALK1 and co-dependent on ACTR-IIA and BMPR-II. Assessment of canonical Smad signalling indicated a reliance of this response on Smad4. Of note, Smad1/5 signalling contributed only at BMP9 concentrations similar to those in the circulation. In the context of inflammation, BMP9 did not alter the induction of CCL2 by TNF-α. As CCL2 promotes monocyte/macrophage chemotaxis and endothelial permeability, these data support the concept that BMP9 preserves basal endothelial integrity. Summary: Two proteins found in the blood, BMP9 and BMP10, reduce the production of CCL2, a protein that recruits inflammatory cells to the blood vessel wall.
Silencing of Wilson Disease gene (ATP7B) induces transcriptional changes in copper-related genes

Wilson Disease is an autosomal recessive disorder of copper metabolism due to mutation in cellular copper transporter - ATP7B. The mutant protein is unable to export copper, leading to its accumulation that results in various harmful molecular changes in cells. In the present study using human hepatoma (HepG2) and neuroblastoma (SH-SY5Y) cells, we report the transcriptional variations in major copper-related genes on ATP7B knockdown. The cells were transfected with specific siRNA to silence ATP7B and the expression of copper-related genes was studied at mRNA level by quantitative real-time PCR. In both cell lines there was significant upregulation of Antioxidant1 (Atox1), human Copper homeostasis protein (hCutC) and Ceruloplasmin (Cp), while the mRNA expression of copper transporter gene hCTR1 (Slc31a1) was not significantly affected. Effect of copper overload was studied by supplying CuSO4 in medium (100 μM/ 24hour) that resulted in further upregulation of these genes. The cell viability was also found to be reduced significantly upon ATP7B silencing. Total cellular copper was estimated by Inductively Coupled Plasma - Atomic Emission Spectrometry (ICPAES). Findings of this study show the alterations in expression of major genes involved in cellular copper network and consequent imbalance in the copper homeostasis during intracellular copper overload.
Risk factors for 2019 novel coronavirus disease (COVID-19) patients progressing to critical illness: a systematic review and meta-analysis

Importance: With the rising number of COVID-19 cases, global health resources are strained by the pandemic. No proven effective therapies or vaccines for this virus are currently available. In order to maximize the use of limited medical resources, distinguishing between mild and severe patients as early as possible has become pivotal. Objective: To systematically review evidence for the risk factors of COVID-19 patients progressing to critical illness. Evidence Review: We conducted a comprehensive search for primary literature in both Chinese and English electronic bibliographic databases. The American agency for health research and quality tool was used for quality assessment. A meta-analysis was undertaken using STATA version 15.0. Results: Twenty articles (4062 patients) were eligible for this systematic review and meta-analysis. First and foremost, we observed that elderly male patients with a high body mass index, high breathing rate and a combination of underlying diseases (such as hypertension, diabetes, cardiovascular disease, and chronic obstructive pulmonary disease) were more likely to develop severe COVID-19 infections. Second, compared with non-severe patients, severe patients had more serious symptoms such as fever and dyspnea. Besides, abnormal laboratory tests were more prevalent in severe patients than in mild cases, such as elevated levels of white blood cell counts, liver enzymes, lactate dehydrogenase, creatine kinase, C-reactive protein and procalcitonin, as well as decreased levels of lymphocytes and albumin. Interpretation: This is the first systematic review exploring the risk factors for severe illness in COVID-19 patients. Our study may be helpful for clinical decision-making and optimizing resource allocation.
Label-Free Bimetallic In Situ Grown 3D Nickel Foam Supported NH2-MIL-88B(Fe2Co)-MOF based Impedimetric Immunosensor for the Detection of Cardiac Troponin I.

In this study, a simple and competent metal-organic framework (MOF) based nickel foam (NF) supported 3D immunosensor (Ab-NH2-MIL-88B(Fe2Co)-MOF/NF) was constructed and utilized for the specific recognition of the biomarker cardiac troponin (I). In the present work, the biosensor fabrication was progressed through the modification of the NF substrate with MOF material (NH2-MIL-88B(Fe2Co)-MOF) to enable amine functionalized electrode. This amine functionalized NF electrodes (NH2-MIL-88B(Fe2Co)-MOF/NF) were then bio-interfaced with anti-cTnI antibodies and ended up as Ab-NH2-MIL-88B(Fe2Co)-MOF/NF electrodes. Analytical executions of the constructed bio-electrode were investigated for the quantitative analysis of cTnI in both buffered and serum solutions. Then, the electrochemical studies were carried out using the electrochemical impedance spectroscopy (EIS) method by monitoring changes concerning the charge transfer resistance (Rct) characteristics. The limit of detection (LOD) of Ab-NH2-MIL-88B(Fe2Co)-MOF/NF immunosensor was achieved to be 13 fg/ml with great specificity. This kind of immunosensor imparts a new platform for the construction and application of MOF-hybrid 3D electrode materials with enhanced electrochemical behavior in cTnI sensing for the first time.
EVALUATION OF THREE SEED FURROW OPENERS MOUNTED ON A ZONE DISK TILLER DRILL FOR RESIDUE MANAGEMENT, SOIL PHYSICAL PROPERTIES AND CROP PARAMETERS

This research was conducted to evaluate the field performance of three newly developed types of furrow opener. Wheat variety, Sehar-2006, was sown in the paddy stubble field. Three types of furrow openers (disk-type, reverse hoe-type, and hoe-type) were fabricated in the department of Farm Machinery and Power and installed on zone disk tiller drill and tested for their performance at three forward speeds of tractor, viz. 3.5 km/hr, 4.75 km/hr and 6.4 km/hr. The impact of furrow openers on residue management, soil physical properties and various crop parameters was evaluated. The mean values of density at the time of seedling emergence at 0-5 cm depth under disk-type furrow opener, reverse-type furrow opener and hoe-type furrow opener were 1.37, 1.35 and 1.34 g/cm 3 and at 5-10 cm depth were 1.48, 1.45 and 1.43 g/cm 3 , respectively. The mean values of moisture content at the time of seedling emergence at 0-5 cm depth under disk-type furrow opener, reverse-type furrow opener and hoe-type furrow opener were 11.86, 11.12 and 10.04% and at 5-10 cm depth were 12.75, 11.26 and 11.07%, respectively. The mean seedling emergence rate index under disk-type furrow opener, reverse-type furrow opener and hoe-type furrow opener was 9.83, 9.42, and 9.33%/day, respectively. The disk-type furrow opener with speed 4.75 km/hr was the better attachment. The mean values of existing residue after 15 days of wheat sowing under disk-type furrow opener, reverse-type furrow opener and hoe-type furrow opener were 10.45, 9.68, and 8.62%, respectively. The measured residue under disk-type furrow opener at 3.5 km/hr speed was 1.08 and 1.22 times greater than that of reverse-type furrow opener and hoe-type furrow opener respectively. The seedling emergence rate index affected the final grain yield. The mean grain yield under disk-type furrow opener, reverse-type furrow opener and hoe-type furrow opener were 4.03, 3.91 and 3.81 t/ha, respectively. The disk-type furrow opener produced the highest grain yield 4.10 t/ha at speed 4.75 km/hr.
Technical Limitations Associated With Molecular Barcoding of Arthropod Bloodmeals Taken From North American Deer Species

Abstract Accurate species-level identification of the source of arthropod bloodmeals is important for deciphering blood feeding patterns of field-collected specimens. Cytochrome c oxidase I (COI) mitochondrial gene sequencing has been used for this purpose; however, species resolution can be difficult to obtain from certain vertebrate genera, including Odocoileus. Sanger sequencing of mitochondrial genes was employed to identify the bloodmeal source of wild-caught mosquitoes trapped in Greeley, Colorado. Initial sequencing of the COI gene of mitochondrial DNA in bloodmeals was inadequate for species-level resolution of bloodmeals from deer in the genus Odocoileus, with current databases returning low fidelity matches to multiple genera. The use of the hypervariable D loop of the control region provided species-level identification of white-tailed deer (Order: Artiodactyla, Family: Cervidae, Odocoileus virginianus); however, taxonomic identification was successful only to genus for mule (O. hemionus hemionus) and black-tailed deer (O. hemionus columbianus). We advocate the use of multiple loci for bloodmeal analysis and the buildout of available databases to include multiple mitochondrial reference genes for reliable host species identification.
Water Developments and Desert Bighorn Sheep: Implications for Conservation

Abstract In recent times the construction and maintenance of wildlife water developments for the stated purpose of conserving desert bighorn sheep (Ovis canadensis) populations has been controversial, especially within sensitive lands of the southwestern United States. A major portion of the controversy is whether wildlife water developments provide a benefit to populations of desert bighorn sheep and whether the associated incursion into the naturalness of an area is justified. Desert bighorn sheep are a valued natural resource and they exist today in small, isolated populations threatened with a variety of human-related impacts (e.g., disease, development, climate change, habitat fragmentation, water diversion). In this article I summarize the available published literature related to desert bighorn sheep and wildlife water developments and review the effects and consequences of water developments in desert bighorn sheep conservation. Based on my review, I contend that recent criticism of water developments has failed to adequately consider anthropogenic factors that can influence wildlife populations and their habitats. My review found that desert bighorn sheep benefit from water developments and that the role of active management of wildlife habitat, including the development of free-standing water for bighorn sheep where this component is unavailable, is justified as a means of mitigating negative anthropogenic influences in an otherwise natural setting.
Macrofaunal control of microbial community structure in continental margin sediments

Significance The majority of the seafloor is bioturbated by macrofauna and most organic carbon mineralization in marine sediments is performed by microorganisms inhabiting bioturbated sediment. However, little is known about how sediment macrofauna influence the community structure of these microorganisms. We show that microbial community composition differs systematically between bioturbated and nonbioturbated sediments across divergent continental margin settings. While microbial communities in bioturbated surface sediments are regulated by macrofauna-controlled geochemical variables, subsurface microbial communities show site-related trends, which correspond to differences in organic carbon sources. Our study produces insights into the controls on microbial community structure in marine sediments. Such insights are necessary to understand the inner workings of the global carbon cycle. Through a process called “bioturbation,” burrowing macrofauna have altered the seafloor habitat and modified global carbon cycling since the Cambrian. However, the impact of macrofauna on the community structure of microorganisms is poorly understood. Here, we show that microbial communities across bioturbated, but geochemically and sedimentologically divergent, continental margin sites are highly similar but differ clearly from those in nonbioturbated surface and underlying subsurface sediments. Solid- and solute-phase geochemical analyses combined with modeled bioturbation activities reveal that dissolved O2 introduction by burrow ventilation is the major driver of archaeal community structure. By contrast, solid-phase reworking, which regulates the distribution of fresh, algal organic matter, is the main control of bacterial community structure. In nonbioturbated surface sediments and in subsurface sediments, bacterial and archaeal communities are more divergent between locations and appear mainly driven by site-specific differences in organic carbon sources.
SoilScanner: 3D Visualization for Soil Profiling using Portable X-ray Fluorescence

Soil scientists perform similar types of exploratory analysis repeatedly, such as generating the spatial distribution of chemical elements. The soil analysis process is time-consuming (may take days or weeks), labor-intensive (involving many people with different expertise for data collection, measurements, visual representation, and data analysis), and involving various tools (from traditional software, such as Microsoft Excel, to some complicated packages such as ArcGIS and MatLab). Inspired by medical scanning, this paper proposes a 3D visual solution, which can be generated via a web interface, allowing Soil scientists to perform on-the-ﬁeld analysis. Our visualization prototype, named SoilScanner, supports a full range of interactive operations, such as ranking, ﬁltering, brushing and linking, and detail on demand. We also demonstrated the usability of our SoilScanner visualizations on the soil proﬁles in West Texas, USA, collected via portable X-ray ﬂuorescence spectrometers.
A Graph Auto-encoder Model of Derivational Morphology

There has been little work on modeling the morphological well-formedness (MWF) of derivatives, a problem judged to be complex and difficult in linguistics. We present a graph auto-encoder that learns embeddings capturing information about the compatibility of affixes and stems in derivation. The auto-encoder models MWF in English surprisingly well by combining syntactic and semantic information with associative information from the mental lexicon.
Efficient Pairwise Annotation of Argument Quality

We present an efficient annotation framework for argument quality, a feature difficult to be measured reliably as per previous work. A stochastic transitivity model is combined with an effective sampling strategy to infer high-quality labels with low effort from crowdsourced pairwise judgments. The model’s capabilities are showcased by compiling Webis-ArgQuality-20, an argument quality corpus that comprises scores for rhetorical, logical, dialectical, and overall quality inferred from a total of 41,859 pairwise judgments among 1,271 arguments. With up to 93% cost savings, our approach significantly outperforms existing annotation procedures. Furthermore, novel insight into argument quality is provided through statistical analysis, and a new aggregation method to infer overall quality from individual quality dimensions is proposed.
Cross-modal Coherence Modeling for Caption Generation

We use coherence relations inspired by computational models of discourse to study the information needs and goals of image captioning. Using an annotation protocol specifically devised for capturing image–caption coherence relations, we annotate 10,000 instances from publicly-available image–caption pairs. We introduce a new task for learning inferences in imagery and text, coherence relation prediction, and show that these coherence annotations can be exploited to learn relation classifiers as an intermediary step, and also train coherence-aware, controllable image captioning models. The results show a dramatic improvement in the consistency and quality of the generated captions with respect to information needs specified via coherence relations.
Max-Margin Incremental CCG Parsing

Incremental syntactic parsing has been an active research area both for cognitive scientists trying to model human sentence processing and for NLP researchers attempting to combine incremental parsing with language modelling for ASR and MT. Most effort has been directed at designing the right transition mechanism, but less has been done to answer the question of what a probabilistic model for those transition parsers should look like. A very incremental transition mechanism of a recently proposed CCG parser when trained in straightforward locally normalised discriminative fashion produces very bad results on English CCGbank. We identify three biases as the causes of this problem: label bias, exposure bias and imbalanced probabilities bias. While known techniques for tackling these biases improve results, they still do not make the parser state of the art. Instead, we tackle all of these three biases at the same time using an improved version of beam search optimisation that minimises all beam search violations instead of minimising only the biggest violation. The new incremental parser gives better results than all previously published incremental CCG parsers, and outperforms even some widely used non-incremental CCG parsers.
Knowledge Supports Visual Language Grounding: A Case Study on Colour Terms

In human cognition, world knowledge supports the perception of object colours: knowing that trees are typically green helps to perceive their colour in certain contexts. We go beyond previous studies on colour terms using isolated colour swatches and study visual grounding of colour terms in realistic objects. Our models integrate processing of visual information and object-specific knowledge via hard-coded (late) or learned (early) fusion. We find that both models consistently outperform a bottom-up baseline that predicts colour terms solely from visual inputs, but show interesting differences when predicting atypical colours of so-called colour diagnostic objects. Our models also achieve promising results when tested on new object categories not seen during training.