Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic regions of durum wheat involved in water productivity

Abstract Durum wheat is a staple food in the Mediterranean Basin, mostly cultivated under rainfed conditions. As such, the crop is often exposed to moisture stress. Therefore, the identification of genetic factors controlling the capacity of genotypes to convert moisture into grain yield (i.e., water productivity) is quintessential to stabilize production despite climatic variations. A global panel of 384 accessions was tested across 18 Mediterranean environments (in Morocco, Lebanon, and Jordan) representing a vast range of moisture levels. The accessions were assigned to water responsiveness classes, with genotypes ‘Responsive to Low Moisture’ reaching an average +1.5 kg ha–1 mm–1 yield advantage. Genome wide association studies revealed that six loci explained most of this variation. A second validation panel tested under moisture stress confirmed that carrying the positive allele at three loci on chromosomes 1B, 2A, and 7B generated an average water productivity gain of +2.2 kg ha–1 mm–1. These three loci were tagged by kompetitive allele specific PCR (KASP) markers, and these were used to screen a third independent validation panel composed of elites tested across moisture stressed sites. The three KASP combined predicted up to 10% of the variation for grain yield at 60% accuracy. These loci are now ready for molecular pyramiding and transfer across cultivars to improve the moisture conversion of durum wheat.
PLK1 inhibition dampens NLRP3 inflammasome–elicited response in inflammatory disease models

Unabated activation of the NLR family pyrin domain–containing 3 (NLRP3) inflammasome is linked with the pathogenesis of various inflammatory disorders. Polo-like kinase 1 (PLK1) has been widely studied for its role in mitosis. Here, using both pharmacological and genetic approaches, we demonstrate that PLK1 promoted NLRP3 inflammasome activation at cell interphase. Using an unbiased proximity-dependent biotin identification (Bio-ID) screen for the PLK1 interactome in macrophages, we show an enhanced proximal association of NLRP3 with PLK1 upon NLRP3 inflammasome activation. We further confirmed the interaction between PLK1 and NLRP3 and identified the interacting domains. Mechanistically, we show that PLK1 orchestrated the microtubule-organizing center (MTOC) structure and NLRP3 subcellular positioning upon inflammasome activation. Treatment with a selective PLK1 kinase inhibitor suppressed IL-1β production in in vivo inflammatory models, including LPS-induced endotoxemia and monosodium urate–induced peritonitis in mice. Our results uncover a role of PLK1 in regulating NLRP3 inflammasome activation during interphase and identify pharmacological inhibition of PLK1 as a potential therapeutic strategy for inflammatory diseases with excessive NLRP3 inflammasome activation.
The genetic identity of neighboring plants in intraspecific mixtures modulates disease susceptibility of both wheat and rice

Mixing crop cultivars has long been considered as a way to control epidemics at the field level and is experiencing a revival of interest in agriculture. Yet, the ability of mixing to control pests is highly variable and often unpredictable in the field. Beyond classical diversity effects such as dispersal barrier generated by genotypic diversity, several understudied processes are involved. Among them is the recently discovered neighbor-modulated susceptibility (NMS), which depicts the phenomenon that susceptibility in a given plant is affected by the presence of another healthy neighboring plant. Despite the putative tremendous importance of NMS for crop science, its occurrence and quantitative contribution to modulating susceptibility in cultivated species remains unknown. Here, in both rice and wheat inoculated in greenhouse conditions with foliar fungal pathogens considered as major threats, using more than 200 pairs of intraspecific genotype mixtures, we experimentally demonstrate the occurrence of NMS in 11% of the mixtures grown in experimental conditions that precluded any epidemics. Thus, the susceptibility of these 2 major crops results from indirect effects originating from neighboring plants. Quite remarkably, the levels of susceptibility modulated by plant–plant interactions can reach those conferred by intrinsic basal immunity. These findings open new avenues to develop more sustainable agricultural practices by engineering less susceptible crop mixtures thanks to emergent but now predictable properties of mixtures.
Green Tea-Derived Catechins Suppress the Acid Productions of Streptococcus mutans and Enhance the Efficiency of Fluoride

Green tea-derived catechins, which can be divided into galloylated (epicatechin gallate: ECG, epigallocatechin gallate: EGCG) and non-galloylated (catechin: C, epicatechin: EC, epigallocatechin: EGC) catechins, are considered to be the main contributors to the caries control potential of green tea. In this study, we intended to compare the antimicrobial effects of these representative green tea-derived catechins and their combined effects with fluoride on the acid production and aggregation of Streptococcus mutans. The effects of different catechins on the growth, aggregation and acid production of S. mutans, and the combined effect of catechins and potassium fluoride (2 mm at pH 7.0, 0.3 mm at pH 5.5) on S. mutans acid production were measured by anaerobic culture, turbidity changes due to aggregation, and pH-stat methods. Molecular docking simulations were also performed to investigate the interactions between catechins and membrane-embedded enzyme II complex (EIIC), a component of the phosphoenolpyruvate-dependent phosphotransferase system (sugar uptake-related enzyme). ECG or EGCG at 1 mg/mL significantly inhibited the growth of S. mutans, induced bacterial aggregation, and decreased glucose-induced acid production (p < 0.05). All catechins were able to bind to EIIC in silico, in the following order of affinity: EGCG, ECG, EGC, EC, and C. Furthermore, they enhanced the inhibitory effects of fluoride at pH 5.5 and significantly inhibited S. mutans acid production by 47.5–86.6% (p < 0.05). These results suggest that both galloylated and non-galloylated catechins exhibit antimicrobial activity, although the former type demonstrates stronger activity, and that the caries control effects of green tea may be due to the combined effects of multiple components, such as catechins and fluoride. The detailed mechanisms underlying these phenomena and the in vivo effect need to be explored further.
Bazzoni’s conjecture and almost Prüfer domains

Abstract An almost Prüfer domain D is an integral domain in which for any , there is an integer such that is invertible. Hence, Prüfer domains are almost Prüfer. An integral domain D is of finite character if each nonzero nonunit of D is contained in only finitely many maximal ideals of D. Bazzoni’s conjecture states that if every nonzero locally principal ideal of a Prüfer domain D is invertible, then D is of finite character. This conjecture was proved in [Holland, Martinez, McGovern and Tesemma, Bazzoni’s Conjecture, J. Algebra 320 (2008), 1764–1768]. In this paper, we show that Bazzoni’s conjecture is true for almost Prüfer domains, that is, we prove that if every locally finitely generated ideal of an almost Prüfer domain D is finitely generated, then D is of finite character. This result will be proved in a more general setting of almost Prüfer v-multiplication domains.
Redescription of an endemic mahseer, Tor mahanadicus (David, 1953) from Mahanadi River basin, India based on integrated morphological and molecular techniques

Tor mahanadicus was originally described as Tor mosal mahanadicus with inadequate information on its morphological traits and no designated type specimen. Currently, T. mahanadicus is synonymized with Tor putitora, solely based on partial molecular data despite significant morphological differences. In this study, we performed an integrated morphological and molecular analysis to redescribe T. mahanadicus from the Mahanadi River. Tor mahanadicus is distinguished from all known Indian Tor species by the presence of 2 complete rows of scales between pelvic fin origin and lateral line, small eye (15.3–16.9% in head length), and a wide mouth gap (21.7–23.8% in head length). Moreover, it undoubtedly distinguished from the closely related species Tor putitora by having a wider body depth (26.8–28.2% in standard length vs. 14.5–19.9%), short snout length (23.3–26.4% in head length vs. 28.0–29.3%) and wide inter orbit space (30.5–37.3% in head length vs. 27.6–28.5%). Additionally, the molecular phylogenetic tree generated from a combination of three genes demonstrates a monophyletic clade separate from the Tor putitora clade. Based on the distinct morphological traits and mitochondrial gene sequences, we established Tor mahanadicus as separate species under the genus Tor.
Medieval Climate in the Eastern Mediterranean: Instability and Evidence of Solar Forcing

This paper examines the hydroclimate history of the Eastern Mediterranean (EM) region during the 10th to 14th centuries C.E. , a period known as the Medieval Climate Anomaly (MCA), a time of significant historical turmoil and change in the region. The study assembles several regional hydroclimatic archives, primarily the Dead Sea reconstructed lake level curve together with the recently extracted deep-lake sediment record, the Soreq Cave speleothem record and its counterpart, the EM marine sediment record and the Cairo Nilometer record of annual maximum summer flood levels in lower Egypt. The Dead Sea record is a primary indicator of the intensity of the EM cold-season storm activity while the Nilometer reflects the intensity of the late summer monsoon rains over Ethiopia. These two climate systems control the annual rainfall amounts and water availability in the two regional breadbaskets of old, in Mesopotamia and Egypt. The paleoclimate archives portray a variable MCA in both the Levant and the Ethiopian Highlands with an overall dry, early-medieval climate that turned wetter in the 12th century C.E. However, the paleoclimatic records are markedly punctuated by episodes of extreme aridity. In particular, the Dead Sea displays extreme low lake levels and significant salt deposits starting as early as the 9th century C.E. and ending in the late 11th century. The Nile summer flood levels were particularly low during the 10th and 11th centuries, as is also recorded in a large number of historical chronicles that described a large cluster of droughts that led to dire human strife associated with famine, pestilence and conflict. During that time droughts and cold spells also affected the northeastern Middle East, in Persia and Mesopotamia. Seeking an explanation for the pronounced aridity and human consequences across the entire EM, we note that the 10th–11th century events coincide with the medieval Oort Grand Solar Minimum, which came at the height of an interval of relatively high solar irradiance. Bringing together other tropical and Northern Hemisphere paleoclimatic evidence, we argue for the role of long-term variations in solar irradiance in shaping the early MCA in the EM and highlight their relevance to the present and near-term future.
Relationships of platelet glycoprotein specific antibody with therapeutic efficacy of short-term high-dose dexamethasone and bleeding score in the newly diagnosed adult patients with primary immune thrombocytopenia

ABSTRACT Objectives: We aimed to investigate relationships of platelet glycoprotein (GP) specific antibody with therapeutic efficacy of high-dose dexamethasone (HD-DXM) and bleeding score in primary immune thrombocytopenia (ITP) adults. Methods: A retrospective study was carried out to analyze relationships of polymorphism of GP specific antibody with initial therapeutic efficacy of HD-DXM and bleeding score of newly diagnosed ITP adults between 1 June, 2016 and 31 January, 2020. Results: 59 patients were involved in the study, with 33 cases of responders and 26 cases of non-responders between June 2016 and January 2020. At admission, there were 31 (52.5%) GP antibody-positive patients. Initial therapy of HD-DXM was effective for 78.6% GP antibody-negative patients and 35.5% GP antibody-positive patients, with a better therapeutic efficacy in patients with anti-GP Ib/IX antibody or anti-GP IIb/IIIa antibody but not in those with anti-GP Ib/IX antibody plus anti-GP IIb/IIIa antibody. Notably, therapeutic efficacy is much worse for minority (Uyghur) patients compared with corresponding Han patients. Similarly, it was much lower in GP antibody-positive patients compared with corresponding negative ones at low and medium bleeding score, with no response in GP antibody-positive patients at high bleeding score. Furthermore, there was a moderate negative correlation between therapeutic efficacy and GP-specific antibody (p < 0.05), but no obvious linear relationship between clinical bleeding degree and GP-specific antibody (p > 0.05). Conclusion: Collectively, the newly diagnosed ITP adults with GP-specific antibody have a poor response to short-term HD-DXM, especially in minority (Uyghur) patients with GP-specific antibody in China.
SPdel: A pipeline to compare and visualize species delimitation methods for single‐locus datasets

An accurate species delimitation is critical for biological studies. In this context, the use of molecular techniques along with species delimitation methods would help to a rapid and accurate biodiversity assessment. The species delimitation methods cluster data sets of orthologous sequences in molecular operational taxonomic units (MOTU). In particular, the methods based on a single gene are easily integrated with the widely used DNA barcoding approach. We developed SPdel a user‐friendly pipeline to integrate different single‐gene species delimitation methods. SPdel is designed to calculate and compare MOTUs obtained by different species delimitation approaches. SPdel also outputs diverse ready‐to‐publish quality figures, that facilitate the interpretation of results. SPdel aims to help researchers use species delimitation methods that would improve biodiversity studies.
Indoor Air: Quality and Control

This timely guide covers the various types of indoor air pollution posing serious health risk to humans and demonstrates today's most effective methods for controlling the quality of indoor air. KEY TOPICS: It covers: risk assessment . organic and inorganic pollutants . heavy metals . respirable particulates . bioaerosols . radon . absorption applications . and adsorption methods. An ideal reference for mechanical, chemical, and environmental engineers.
Research on evolution process of full-layer incision of skin tissue under different laser incidences.

Considering difficulties of achieving vertical incidence of beam in different positions of skin, it's significant to study potential effects of incidence angles of laser on incisions. Surgical platform with a 1064nm continuous fiber laser was established. Incident angle was adopted and real-time temperature fluctuations in laser operating area could be monitored. The rats were treated with laser at day 0 and day 3 after incision modeling, and H&E, Masson, Sirius Red and Immuno-histochemical staining and enzyme-linked immunosorbent assay were adopted at day 3,7,14 to analyze the performance of healing. Laser with energy density of 67.54J/mm2 can effectively accelerate wound healing in vivo, in which laser with incident angle around 60° can effectively avoid scar hyperplasia. Therefore, the use of low energy laser with small deflection angle has a good clinical application prospect in promoting wound healing. This article is protected by copyright. All rights reserved.
Comparative study of the glistening between four intraocular lens models assessed by OCT and deep learning

Using a DL-based algorithm, it is possible to quantify, classify, and compare the glistening severity in different IOL models using OCT images in a simple and objective manner. Purpose: To evaluate the glistening in 4 different models of intraocular lenses (IOLs) using optical coherence tomography (OCT) and deep learning (DL). Setting: Centro Internacional de Oftalmología Avanzada (Madrid, Spain). Design: Cross-sectional study. Methods: 325 eyes were assessed for the presence and severity of glistening in 4 IOL models: ReSTOR+3 SN6AD1 (n = 41), SN60WF (n = 110), PanOptix TFNT (n = 128) and Vivity DFT015 (n = 46). The presence of glistening was analyzed using OCT, identifying the presence of hyperreflective foci (HRF) in the central area of the IOL. A manual and an original DL-based quantification algorithm designed for this purpose was applied. Results: Glistening was detected in 22 (53.7%) ReSTOR SN6AD1, 44 (40%) SN60WF, 49 (38.3%) PanOptix TFNT, and 4 (8.7%) Vivity DFT015 IOLs, when any grade was considered. In the comparison of the different types of IOLs, global glistening measured as total HRF was 17.3 ± 25.9 for the ReSTOR+3; 9.3 ± 15.7 for the SN60WF; 6.9 ± 10.5 for the PanOptix; and 1.2 ± 2.6 for the Vivity (P < .05). There was excellent agreement between manual and DL-based quantification (≥0.829). Conclusions: It is possible to quantify, classify and compare the glistening severity in different IOL models using OCT images in a simple and objective manner with a DL algorithm. In the comparative study, the Vivity presented the lowest severity of glistening.
Machine Learning Analysis of Raman Spectra To Quantify the Organic Constituents in Complex Organic–Mineral Mixtures

Important decisions in local agricultural policy and practice often hinge on the soil’s chemical composition. Raman spectroscopy offers a rapid noninvasive means to quantify the constituents of complex organic systems. But the application of Raman spectroscopy to soils presents a multifaceted challenge due to organic/mineral compositional complexity and spectral interference arising from overwhelming fluorescence. The present work compares methodologies with the capacity to help overcome common obstacles that arise in the analysis of soils. We created conditions representative of these challenges by combining varying proportions of six amino acids commonly found in soils with fluorescent bentonite clay and coarse mineral components. Referring to an extensive data set of Raman spectra, we compare the performance of the convolutional neural network (CNN) and partial least-squares regression (PLSR) multivariate models for amino acid composition. Strategies employing volume-averaged spectral sampling and data preprocessing algorithms improve the predictive power of these models. Our average test R2 for PLSR models exceeds 0.89 and approaches 0.98, depending on the complexity of the matrix, whereas CNN yields an R2 range from 0.91 to 0.97, demonstrating that classic PLSR and CNN perform comparably, except in cases where the signal-to-noise ratio of the organic component is very low, whereupon CNN models outperform. Artificially isolating two of the most prevalent obstacles in evaluating the Raman spectra of soils, we have characterized the effect of each obstacle on the performance of machine learning models in the absence of other complexities. These results highlight important considerations and modeling strategies necessary to improve the Raman analysis of organic compounds in complex mixtures in the presence of mineral spectral components and significant fluorescence.
The Effect of Staged Versus Usual Care Physiotherapy on Knee Function Following Anterior Cruciate Ligament Reconstruction.

CONTEXT The long duration and high cost of anterior cruciate ligament reconstruction (ACLR) rehabilitation can pose barriers to completing rehabilitation, the latter stages of which progress to demanding sport-specific exercises critical for a safe return to sport. A staged approach shifting in-person physiotherapy sessions to later months of recovery may ensure patients undergo the sport-specific portion of ACLR rehabilitation. Design/Objective: To compare postoperative outcomes of knee function in patients participating in a staged ACLR physiotherapy program to patients participating in usual care physiotherapy through a randomized controlled trial. METHODS One hundred sixty-two patients were randomized to participate in staged (n = 80) or usual care physiotherapy (n = 82) following ACLR and assessed preoperatively and postoperatively at 2 weeks, 6 weeks, 3 months, and 6 months. The staged group completed the ACLR rehabilitation protocol at home for the first 3 months, followed by usual care in-person sessions. The usual care group completed in-person sessions for their entire rehabilitation. Outcome measures included the Lower Extremity Functional Scale, International Knee Documentation Committee Questionnaire, pain, range of motion, strength, and hop testing. RESULTS There were no statistically significant between-group differences in measures of knee function at 6 months postoperative. Patients in the usual care group reported significantly higher International Knee Documentation Committee scores at 3 months postoperative (mean difference = 5.8; 95% confidence interval, 1.3 to 10.4; P = .01). CONCLUSION A staged approach to ACLR rehabilitation does not appear to impede knee function at 6 months postoperative but may result in worse patient reported outcomes at early follow-ups.
Identification of the SNARE complex that mediates the fusion of multivesicular bodies with the plasma membrane in exosome secretion

Abstract Exosomes play crucial roles in local and distant cellular communication and are involved in various physiological and pathological processes. Tumour‐derived exosomes are pivotal to tumorigenesis, but the precise mechanisms underlying their secretion remain elusive. In particular, the SNARE proteins that mediate the fusion of multivesicular bodies (MVBs) with the plasma membrane (PM) in tumour cells are subject to debate. In this study, we identified syntaxin‐4, SNAP‐23, and VAMP‐7 as the SNAREs responsible for exosome secretion in MCF‐7 breast cancer cells and found that a SNARE complex consisting of these SNAREs can drive membrane fusion in vitro. Deletion of any of these SNAREs in MCF‐7 cells did not affect MVB biogenesis and transportation, indicating their specific involvement in MVB–PM fusion. In addition, syntaxin‐4, SNAP‐23, and VAMP‐7 play equivalent roles in exosome secretion in both HeLa cervical cancer cells and A375 melanoma cells, suggesting their conserved function in exosome secretion. Furthermore, deletion of VAMP‐7 in 4T1 mammary carcinoma cells efficiently inhibited exosome secretion and led to significant attenuation of tumour growth and lung metastasis in mouse models, implying that VAMP‐7 may hold promise as a novel therapeutic target for breast cancer.
Gastrointestinal organs and organoids-on-a-chip: advances and translation into the clinics

Microfluidic organs and organoids-on-a-chip models of human gastrointestinal systems have been established to recreate adequate microenvironments to study physiology and pathophysiology. In the effort to find more emulating systems and less costly models for drugs screening or fundamental studies, gastrointestinal system organoids-on-a-chip have arisen as promising pre-clinical in vitro model. This progress has been built on the latest developments of several technologies such as bioprinting, microfluidics, and organoid research. In this review, we will focus on healthy and disease models of: human microbiome-on-a-chip and its rising correlation with gastro pathophysiology; stomach-on-a-chip; liver-on-a-chip; pancreas-on-a-chip; inflammation models, small intestine, colon and colorectal cancer organoids-on-a-chip and multi-organoids-on-a-chip. The current developments related to the design, ability to hold one or more ‘organs’ and its challenges, microfluidic features, cell sources and whether they are used to test drugs are overviewed herein. Importantly, their contribution in terms of drug development and eminent clinical translation in precision medicine field, Food and Drug Administration approved models, and the impact of organoid-on-chip technology in terms of pharmaceutical research and development costs are also discussed by the authors.