Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors

Wheat grain development after anthesis is an important biological process, in which major components of seeds are synthesised, and these components are further required for germination and seed vigour. We have made a comparative RNA-Seq analysis between hexaploid wheat and its individual diploid progenitors to know the major differentially expressed genes (DEGs) involved during grain development. Two libraries from each species were generated with an average of 55.63, 55.23, 68.13, and 103.81 million reads, resulting in 79.3K, 113.7K, 90.6K, and 121.3K numbers of transcripts in AA, BB, DD, and AABBDD genome species respectively. Number of expressed genes in hexaploid wheat was not proportional to its genome size, but marginally higher than that of its diploid progenitors. However, to capture all the transcripts in hexaploid wheat, sufficiently higher number of reads was required. Functional analysis of DEGs, in all the three comparisons, showed their predominance in three major classes of genes during grain development, i.e., nutrient reservoirs, carbohydrate metabolism, and defence proteins; some of them were subsequently validated through real time quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Further, developmental stage–specific gene expression showed most of the defence protein genes expressed during initial developmental stages in hexaploid contrary to the diploids at later stages. Genes related to carbohydrates anabolism expressed during early stages, whereas catabolism genes expressed at later stages in all the species. However, no trend was observed in case of different nutrient reservoirs gene expression. This data could be used to study the comparative gene expression among the three diploid species and homeologue-specific expression in hexaploid.
1H-NMR-based urine metabolomics reveals signs of enhanced carbon and nitrogen recycling in prostate cancer.

Prostate cancer is the second most common tumor, and the fifth cause of cancer-related death among men worldwide. PC cells exhibit profound signaling and metabolic reprogramming that accounts for the acquisition of aggressive features. Whereas the metabolic understanding of this disease has increased in recent years, the analysis of such alterations through non-invasive methodologies in biofluids remains limited. Here we used NMR-based metabolomics on a large cohort of urine samples (more than 650) from PC and benign prostate hyperplasia patients to investigate the molecular basis of this disease. Multivariate analysis failed to distinguish between the two classes, highlighting the modest impact of prostate alterations on urine composition and the multifactorial nature of PC. Yet, univariate analysis of urine metabolites unveiled significant changes, discriminating PC from BPH. Metabolites with altered abundance in urine from PC patients revealed changes in pathways related to cancer biology, including glycolysis and the urea cycle. We found out that metabolites from such pathways were diminished in the urine from PC individuals, strongly supporting the notion that PC reduces nitrogen and carbon waste in order to maximize their usage in anabolic processes that support cancer cell growth.
Effects of Naphthaleneacetic Acid and Benzyladenine on Growth of Bulblets Regenerated from White Callus of Mother Scale of Lilium japonicum Thunb.

White callus induced from mother scale of Lilium japonicum Thunb. was cultured on MS-medium without plant hormones under continuous 2000 lx at 25 •Ž in vitro. A bulblet regenerated on the white callus was used for treatments. 1. Small bulblets, 15 to 18 mg (FW), were imbedded on MS-media containing of NAA (0.2, 1.0 and 5.0ppm) and BA (0.2, 1.0 and 5.0ppm), and then cultured for 8 weeks. The grown bulblets could be classified into three types; normal type, abnormal type-I and abnormal type-II. The morphology of normalbulblets was comparable to bulblets that formed on mother scales cultured in vitro.The bulblets of abnormal type-I were globular and the scale grew more slowly than that of normal ones. Scale of the type-II became dropsy and grew very slowly. 2. The regenerated bulblets which were cultured on a medium of 0.1 ppm NAA and 0.01 ppm BA gained the most fresh weight and had the most and longest roots per bulblet compared to the other treatments. Leaf emergence was advanced by the medium of 0.01 ppm NAA and 0.1 ppm BA. Histologically, root tips of bulblets grown on the medium of 1.0 ppm NAA and no BA for 8 weeks had two central cylinders, and a large hollow core in the cortex. Cracks in the epidermis also developed on this medium. 3. When the bulblets with scale leaves were cultured on the medium of 0.1 ppm NAA and no BA for 4 weeks, they has grown into a plantlet with roots. We conclude that the combination of 0.1 to 0.01 of NAA and BA, respectively, were optimum for the growth and rooting of bulblets.
The Association of Physical Activity with Cardiovascular Events and Mortality Mediated by Diabetes in Older Mexican Americans.

Low physical activity (PA) among older adults increases the risk of cardiovascular disease (CVD) and mortality through metabolic disorders such as type 2 diabetes. We aimed to elucidate the extent to which diabetes mediates the effect of non-occupational PA levels on CVD and mortality among older Mexican Americans. This study included 1,676 adults from the Sacramento Area Latino Study on Aging (1998-2007). We employed Cox proportional hazards regression models to investigate associations of PA levels with all-cause mortality, fatal CVD, and nonfatal CVD events. Utilizing causal mediation analysis within counterfactual framework, we decomposed the total effect of PA into natural indirect and direct effects. Over follow-up (median 8 years), low PA (<25th percentile) was associated with the increased risk for all-cause mortality (HR, 1.36; 95% CI, 1.06-1.75), fatal CVD (HR, 2.05; 95% CI, 1.42-2.97) and nonfatal CVD (HR, 1.67; 95% CI, 1.18-2.37), compared to high PA (≥75th percentile). Diabetes mediated 11.0%, 7.4%, and 5.2% of the total effect of PA on all-cause mortality, fatal CVD, and nonfatal CVD events, respectively. Our findings indicate that public health interventions targeting diabetes prevention and management would be a worthwhile strategy to prevent cardiovascular disease and mortality among older Mexican Americans with insufficient PA levels.
Tumour‐immune microenvironment in duodenal‐type follicular lymphoma

Despite duodenal‐type follicular lymphoma (DTFL) being morphologically, immunophenotypically and genetically indistinguishable from nodal FL (nFL), this entity typically shows a significantly better prognosis. Here, we analysed the tumour immune microenvironments of diagnostic specimens from patients with DTFL (n = 30), limited‐stage FL (LSFL; n = 19) and advanced‐stage FL (ASFL; n = 31). The mean number of CD8+ tumour‐infiltrating lymphocytes (TILs) in the neoplastic follicles was higher in DTFL (1,827/mm2) than in LSFL (1,150/mm2) and ASFL (1,188/mm2) (P = 0·002, P = 0·002, respectively). In addition, CD8+PD1− T cells with non‐exhausting phenotype were more abundant in the peripheral blood (PB) of DTFL than in LSFL and ASFL, indicating that DTFL may exhibit a better and longer‐lasting T cell‐mediated immune response. Moreover, whereas FOXP3+CTLA‐4+ effector regulatory T cells (eTregs) were rarely observed in the neoplastic follicles of DTFL (mean: 12/mm2), they were more abundant in LSFL (78/mm2) and ASFL (109/mm2) (P = 2·80 × 10−5, P = 4·74 × 10−8, respectively), and the numbers of eTregs correlated inversely with those of CD8+ TILs (r = −0267; P = 0·018). Furthermore, DTFL showed significantly fewer circulating FOXP3hiCD45RA‐CD25hi eTregs (0·146%) than ASFL (0·497%) and healthy controls (0·639%) (P = 0·0003, P = 6·79 × 10−7, respectively). These results suggest that the augmented anti‐tumour immune reactions may contribute to a better prognosis on DTFL.
Angelonia flower mottle, a new disease of Angelonia angustifolia caused by a hitherto unknown carmovirus

), a Central Americanornamental, is receiving increasing attention in the USA and Europe forits attractive ﬂowers. In Germany, a number of accessions from com-mercial companies, subjected to evaluation for varietal release, exhibitedconspicuous ﬂower mottling symptoms, suggestive of virus infection.Carmovirus-like isometric particles (approx. 30 nm in diameter)were detected in plants with symptoms by electron microscopy. Sapinoculation studies revealed that the virus is mechanically transmissibleto Angelonia plants, leading to mottling symptoms on the petals ofﬂowers. When inoculated to Nicotiana hesperis, N. occidentalis, N. gluti-nosa and N. clevelandii , latent infections conﬁned to the site of inoculationsite resulted. An antiserum (DSMZ AS-858) raised against a puriﬁedvirus preparation, reacted speciﬁcally with homologous antigen in westernblot analyses. Virus was detected in ﬂowers and in symptomless leaves.Immunoelectron microscopic decoration tests showed no detectablecross-reaction to several other carmoviruses.Clones of the complete coat protein gene were obtained by RT-PCRfrom viral RNA isolated from puriﬁed particles. Sequence analysis of the1053 nucleotide coat protein gene (EMBL Acc. No. AM050058; encodinga predicted 351 amino acid product) conﬁrmed this virus to be a typical,but distinct, carmovirus with 49 and 48% nucleotide sequence identity(37% and 35 % amino acid sequence identity) to Pelargonium ﬂowerbreak virus and Carnation mottle virus respectively.During cultivation of Angelonia, transient mild chlorotic spots appearedon the leaves of infected and non-infected plants, which are suspected tobe stress-induced. Since the ﬂower mottle symptoms consistently correlatewith infection by the carmovirus, it is proposed naming this tentative newcarmovirus species, Angelonia ﬂower mottle virus. *E-mail: s.winter@bba.de Accepted 5 October 2005 at www.bspp. org.uk/ndr where ﬁgures relating to this paper can be viewed. © 2006 The Authors Journal compilation © 2006 BSPP
Sibling Violence and Psychological Adjustment: The Role of Maladaptive Coping and Maternal Authoritativeness

This study examined the phenomenon of sibling violence in Singapore. The underlying mechanisms through which maternal authoritativeness and maladaptive coping influenced psychological adjustment following sibling violence were also investigated. Questionnaires were administered to 287 female and 128 male Singaporean college students between the ages of 18 to 27. Results showed that lifetime and past-year prevalence estimates of sibling violence in college students in Singapore were 89.9% and 62.0%, respectively. Lifetime psychological sibling violence involvement and past-year sibling violence involvement (both physical and psychological) were significantly related to maladaptive coping and overall psychological adjustment; lifetime sibling violence involvement was significantly related to maternal authoritativeness, anxiety, and depression only. Maladaptive coping was found to be a significant mediator between past-year physical and psychological sibling violence involvement and two measures of psychological adjustment, anxiety and depression. Maternal authoritativeness functioned as a moderator only for the relationship between past-year psychological sibling violence exposure and psychological adjustment. At low but not high levels of maternal authoritativeness, past-year psychological violence involvement was significantly related to higher levels of anxiety and depression, and lower levels of self-esteem. These findings show that sibling violence is a pervasive problem in Asian countries as well, such as in Singapore. There is a need to educate both the public and the relevant authorities so that steps can be taken to protect those who have experienced or are at risk of experiencing such violence. Through elucidating the role of maternal authoritativeness and maladaptive coping, the present study also suggests new avenues for interventions to reduce the adverse effects of sibling violence. Limitations and future directions are also discussed.
CRY1-CBS binding regulates circadian clock function and metabolism

Circadian disruption influences metabolic health. Metabolism modulates circadian function. However, the mechanisms coupling circadian rhythms and metabolism remain poorly understood. Here we report that Cystathionine β-synthase (CBS), a central enzyme in one-carbon metabolism, functionally interacts with the core circadian protein Cryptochrome1 (CRY1). In cells, CBS augments CRY1 mediated repression of the CLOCK/BMAL1 complex and shortens circadian period. Notably, we find that mutant CBS-I278T protein, the most common cause of homocystinuria, does not bind CRY1 or regulate its repressor activity. Transgenic CbsZn/Zn mice, while maintaining circadian locomotor activity period, exhibit reduced circadian power and increased expression of E-BOX outputs. CBS function is reciprocally influenced by CRY1 binding. CRY1 modulates enzymatic activity of the CBS. Liver extracts from Cry1−/− mice show reduced CBS activity that normalizes after the addition of exogenous wild type (WT) CRY1. Metabolomic analysis of WT, CbsZn/Zn, Cry1−/−, and Cry2−/− samples highlights the metabolic importance of endogenous CRY1. We observed temporal variation in one-carbon and transsulfuration pathways attributable to CRY1 induced CBS activation. CBS-CRY1 binding provides a post-translational switch to modulate cellular circadian physiology and metabolic control.
Challenges in Matrix Metalloproteinases Inhibition

Matrix metalloproteinases are enzymes that degrade the extracellular matrix. They have different substrates but similar structural organization. Matrix metalloproteinases are involved in many physiological and pathological processes and there is a need to develop inhibitors for these enzymes in order to modulate the degradation of the extracellular matrix (ECM). There exist two classes of inhibitors: endogenous and synthetics. The development of synthetic inhibitors remains a great challenge due to the low selectivity and specificity, side effects in clinical trials, and instability. An extensive review of currently reported synthetic inhibitors and description of their properties is presented.
Cholinergic Markers and Cytokines in OSA Patients

The role of inflammation and dysfunction of the cholinergic system in obstructive sleep apnea (OSA) has not exhaustively clarified. Thus, in this study, we explore the non-neuronal cholinergic system and the balance of T helper (Th) 17- and T regulatory (Treg)-related cytokines in OSA patients. The study includes 33 subjects with obstructive sleep apnea and 10 healthy controls (HC). The expression levels of cholinergic system component, RAR-related orphan receptor (RORc), transcription factor forkhead box protein 3 (Foxp3) and cytokines were evaluated. Th17- and Treg-related cytokines, choline levels and acetylcholinesterase (AChE), butyrylcholinesterase (BuChE) activity were quantified in OSA and control subjects. AChE and nicotinic receptor α 7 subunit (α7nAChR) gene expression and serum levels of choline, AChE and BuChE were lower in OSA patients than in the HC group. Compared with the HC group, OSA patients exhibited an increased expression, secretion and serum levels of pro-inflammatory cytokines, a reduced expression, secretion and serum levels of transforming growth factor (TGF)β and reduced Foxp3 mRNA levels. The Th17/Treg-related cytokine ratio was higher in the OSA group. Our results confirm and reinforce the hypothesis that OSA may be considered a systemic inflammatory disease, and that an imbalance of non-neuronal cholinergic and pro/anti-inflammatory cytokines may contribute to development and progression of comorbidities in OSA subjects. The evaluation of Th17/Treg-related cytokine may provide an additional explanation for OSA pathogenesis and clinical features, opening new directions for the OSA management.
Hepatoprotective activity of Thymus linearis against paracetamol and carbon tetrachloride-induced hepatotoxicity in albino mice

In the present study, the hepatoprotective activity of aqueous and ether extracts of Thymus linearis (250 and 500 mg/kg orally) was evaluated against carbon tetrachloride- and paracetamol-induced hepatic damage in mice. Serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) were assessed. Antioxidant activity of both the extracts was also determined using 1-1-diphenyl-2-picryl hydrazine (DPPH) scavenging method. The results indicated that both the extracts significantly produce a dose dependent reduction in serum levels of ALT, AST, ALP when compared to carbon tetrachloride-and paracetamol-treated groups. The maximum effect in all the parameters was observed at a dose of 500 mg/kg. The extracts also demonstrated a significant antioxidant activity. LD 50 of both extracts was found to be a 1050 and 900 mg/kg respectively. It is conceivable that the hepatoprotective activity of T. linearis might be due to the presence of certain pharmacologically active compounds.
Ultrafiltration volume by once‐weekly hemodialysis is a predictor of technique survival of combination therapy with peritoneal dialysis and hemodialysis

Overhydration is a major cause of technique failure of peritoneal dialysis (PD). Hence, we investigated the impact of ultrafiltration (UF) volume by once‐weekly hemodialysis (HD), excess volume beyond their dry weight, on technique survival of PD and HD combination therapy (PD+HD). Forty‐six anuric PD+HD patients were divided into three groups according to baseline UF volume by HD: low‐UF (
Diabetes or endocrinopathy admitted in the COVID‐19 ward

The Covid‐19 pandemic confronted us with unknown clinical pictures, also in diabetology and endocrinology. Sharing clinical experiences is therefore of enormous importance. Actually, information about the care given in the Covid‐19 ward (in contrast to that provided in the Emergency Room/ICU) is still sparse. The last weeks we built experience and gathered knowledge while giving hospital care to patients who had a pre‐existent endocrine disease (and diabetes; most patients suffered from a type two diabetes). In our contribution we presented our insights obtained from this intensive period obtained in the Covid‐19 ward.
Age and growth of marbled sole Pleuronectes yokohamae in Harima Nada and Osaka Bay, the Seto Inland Sea, Japan

播磨灘・大阪湾産マコガレイの年齢と成長の関係および調査年による成長の差異ならびに他海域の成長との比較を行った。 また，Walford の定差図法と最小二乗法による成長推定結果の差異について検討した。 最小二乗法で計算された成長式の方がより的確に本種の成長を表していると判断された。 1986～1989 年と 1998～2001 年の比較では，雌雄とも後者の計算体長の方が大きく，両年代間における成長の変異が示唆された。 また，当海域産マコガレイは隣接する紀伊水道北部産に比べて若齢期の成長が早く，極限体長が小さい傾向がみられた。
Carbohydrate utilisation by cell suspension cultures of Phaseolus vulgaris

Uptake of sugar by Phaseolus vulgaris cell suspension cultures from a sucrose supplemented medium is predominantly in the hexose form. This is due to a rapid cleavage of the sucrose by an apoplastic acid invertase activity and an apparent very low demand for and uptake of carbon from the medium prior to induction of cell growth and division. Glucose is preferentially taken up, leading to an accumulation of fructose in the medium. However, when the glucose is depleted the cells do take up the fructose at a rate similar to that of glucose. When glucose or fructose is supplied individually to cell cultures, both are utilised very efficiently with growth slightly better on the fructose medium. Hexose uptake is largely an active process with diffusion uptake even at the highest concentrations (> 50 mM) contributing less than 30%. The hexose uptake system of the cells has a greater affinity for glucose (Km= 240 µM) than for fructose (Km= 960 µM) but the maximum uptake (Vmax) is similar. The major difference in the kinetic properties of hexose uptake is that glucose is a strong inhibitor of fructose uptake, while fructose has little effect on glucose uptake. The differences in the kinetic properties of the uptake system for the two hexoses can largely explain the observed pattern of hexose utilisation when both glucose and fructose are present in the medium.
Long non-coding RNA DSCAM-AS1 upregulates USP47 expression through sponging miR-101-3p to accelerate osteosarcoma progression.

Osteosarcoma (OS) originating from the mesenchymal is one of the most common bone invasive tumors with an extremely high mortality rate. Previous studies have reported that long non-coding RNAs (lncRNAs) play essential roles in the tumorigenesis and progression of a multitude of human cancers. LncRNA DSCAM-AS1 has been reported to be an oncogenic gene in many cancers. However, the role and regulatory mechanism of DSCAM-AS1 in OS have not been investigated deeply. In this study, our findings proved that DSCAM-AS1 was highly expressed in OS cells. DSCAM-AS1 knockdown suppressed cell proliferation, migration and invasion, as well as induced cell apoptosis in OS. Additionally, DSCAM-AS1 suppression inactivated the Wnt/β-catenin pathway. Moreover, researches of molecular mechanism confirmed that DSCAM-AS1 could function as a sponge for miR-101-3p and Ubiquitin-specific peptidase 47 (USP47) was the target gene of miR-101-3p. Furthermore, a negative relationship between miR-101-3p and DSCAM-AS1 or USP47 was discovered. Rescue assays suggested that DSCAM-AS1 regulated OS progression through binding with miR-101-3p to modulate USP47 expression. Finally, we found that AKT/mTOR signal pathway might be a possible principle in mediating DSCAM-AS1 in OS. Taken together, DSCAM-AS1 accelerated OS progression via miR-101-3p/USP47 axis, which might present a new potential therapeutic treatment for OS.
Increasing substrate heterogeneity as a bet‐hedging strategy for restoring wetland vegetation

Mimicking the natural heterogeneity of wetland substrates, e.g. by roughening surface soil or constructing hummocks, has been shown to facilitate wetland plant establishment. We asked if incorporating substrate heterogeneity could also help plants withstand variation in moisture levels. In a wetland with Carex stricta (tussock sedge) as the main restoration target, we manipulated substrates to create different soil moisture environments for planted C. stricta plugs. Our artificial mounds mimicked tussocks formed by C. stricta in natural meadows (circa 10–40 cm in height); we also varied mound compositions and created shallow depressions. Monitoring demonstrated variation in soil moisture among our treatments and natural differences in soil moisture between experimental blocks. Additionally, rainfall varied from severe drought in year 1 to extreme rainfall in year 2. Plug survival, flowering, cover, biomass, leaf length, and growth rate all varied with treatment, block, and/or year. Interactions among those factors were common. Planting plugs in shallow depressions exacerbated stress in a wet block during a wet year, causing low survival. Planting plugs in moisture‐retaining peat pots allowed them to survive and sustain growth even in a dry block during a dry year. We conclude that heterogeneous substrates can be used to hedge against environmental variability by widening the range of microsites available within a restoration site and thereby moderating stressful conditions in some areas.