Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of QTLs for the micromorphology on the seed coat surface of soybean using recombinant inbred lines

Abstract The seed coat of soybean (Glycine max (L.) Merrill) must protect the seed but allow water intake. Overprotection, causing impermeability, is assumed to be due to the presence of an impermeable layer in the seed coat, although validation of this assumption has relied on imbibition testing, which tends to be influenced by microfractures in the seed coat. Recent micromorphological analyses using laser-assisted topography microscopy revealed links to the surface roughness (SR) of the seed coat. To verify genetic links between hardseededness and SR, we analysed quantitative trait loci (QTLs) governing SR formation using 148 recombinant inbred lines (RILs) with a genetic linkage map covering 2663.6 cM of all 20 linkage groups of soybean, with 355 DNA markers and 5 phenotype markers. Five QTLs were detected, including previously identified hardseededness QTLs for ratio of seeds absorbing water, namely RAS1 and RAS2, which accounted for 20% of the phenotypic variance, and one near a locus inhibiting seed coat colour (I). These results indicate that the impermeability of soybean seed is genetically related to the reduction of SR.
L‐type Ca2+ channel opener BayK 8644‐induced Ca2+ influx and Ca2+ release in human oral cancer cells (OC2)

The effect of BayK 8644, a chemical widely used to activate L‐type Ca2+ channels, on cytosolic free Ca2+ concentrations ([Ca2+]i) in human oral cancer cells (OC2) has not been explored to date. The present study examined whether BayK 8644 altered basal [Ca2+]i levels in suspended OC2 cells by using fura‐2. BayK 8644 (10 pM–10 µM) increased [Ca2+]i in a concentration‐dependent manner. The Ca2+ signal was reduced partly by removing extracellular Ca2+. BayK 8644‐induced Ca2+ influx was blocked by nifedipine, but was not altered by the store‐operated Ca2+ entry inhibitors, econazole and SKF96365; protein kinase C modulators phorbol 12‐myristate 13‐acetate (PMA) and GF109203X; the protein kinase A inhibitor H89; and the phospholipase A2 inhibitor, aristolochic acid. In Ca2+‐free medium, after pretreatment with 1 µM BayK 8644, 1 µM thapsigargin (an endoplasmic reticulum Ca2+ pump inhibitor)‐induced [Ca2+]i rises were abolished; and conversely, thapsigargin pretreatment abolished BayK 8644‐induced [Ca2+]i rises. Inhibition of phospholipase C with U73122 did not change BayK 8644‐induced [Ca2+]i rises. Collectively, in OC2 cells, BayK 8644 induced [Ca2+]i rises by causing phospholipase C‐independent Ca2+ release from the endoplasmic reticulum; and Ca2+ influx via L‐type Ca2+ channels. Drug Dev Res 69: 2008. © 2008 Wiley‐Liss, Inc.
Clustering of Lifestyle Factors and Its Association with Low Back Pain: A Cross-Sectional Study of Over 400,000 Japanese Adults

Purpose Although many studies have indicated the association between low back pain (LBP) and lifestyle factors, the combined effect of lifestyle factors on LBP has not been adequately investigated. We aimed to investigate the association between a cluster of unhealthy lifestyle behaviors and LBP using a large cohort of Japanese adults. Methods We included 419,003 adults aged over 20 years who underwent an annual health checkup between April 2013 and March 2014 in Japan. Information on the following lifestyle factors was collected using the standardized questionnaire: smoking, alcohol intake, exercise, physical activity, walking speed, weight control, eating habits, and sleep. Each factor was evaluated as a dichotomous variable (1: health risk, 0: no health risk). A lifestyle risk score was calculated by summing the score of each lifestyle factor (range: 0–12) and was categorized into three groups (low, moderate, high). LBP was defined as self-reported LBP under treatment. Logistic regression analysis was conducted to calculate the odds ratio (OR) and 95% confidence interval (CI) for LBP. Results In multivariable logistic regression analysis, the OR for LBP was significantly higher in the moderate-risk score group (adjusted OR: 1.33 [95% CI: 1.23–1.44] in men; 1.40 [95% CI: 1.27–1.54] in women) and the high-risk score group (adjusted OR: 1.54 [95% CI: 1.43–1.67] in men; 1.83 [95% CI: 1.64–2.03] in women) than in the low-risk score group. A trend of higher risk of LBP associated with higher lifestyle risk score was observed in both sexes (p for trend < 0.001). These results were similar even in subgroup analysis by age and body mass index (BMI). Conclusion Clustering of unhealthy lifestyles was associated with increased risk of LBP regardless of age and BMI. These results may provide implications for better prevention and management of LBP, considering modifiable lifestyle factors.
Characterization of Dextrins obtained by Enzymatic Treatment of Cationic Potato Starch

The substitution pattern of cationic potato starches was studied using starch hydrolyzing enzymes and a characterization of the hydrolysis products. Native and cationic starch samples were hydrolyzed with pullulanase, isoamylase, and α-amylase and the molecular-weight distributions of the resulting dextrins were studied using gel permeation chromatography. Isoamylase hydrolyzed the native potato starch sample readily, whereas hydrolysis with pullulanase was incomplete. Pullulanase hydrolyzed, however, cationic starch with higher DS (degree of substitution) more efficiently than isoamylase. The hydrolysis products obtained with pullulanase were separated according to charge using cation-exchange chromatography into one unbound and two bound fractions. The unbound fraction possessed an increasing number of short chains from amylopectin with increasing DS of the starch sample. The bound material contained amylose and dextrins with sizes corresponding to the long B-chains. The high portion of uncharged dextrins after α-amylolysis suggested that the substitution pattern, on the molecular level, was non-random. The composition of the unbound and bound material, obtained by ion-exchange chromatography of α-amylase treated starches, suggested a more intense fragmentation with increasing DS of the sample. Possibly, the substituents influence substrate conformation and thereby alter the hydrolysis patterns. It is concluded that a thorough understanding of the enzymatic hydrolysis patterns is of ultimate importance in structural studies of modified starch.
Natal trace‐elemental signatures in the otoliths of an open‐coast fish

We show that chemical differences found along the open coast are sufficiently strong to leave a readable natal signature in fish otoliths. Laser ablation inductively coupled plasma mass spectrometric (LA‐ICPMS) analysis of individual larval otoliths taken from near‐term females of the primitively viviparous rockfish Sebastes atrovirens indicates detectable levels of several trace elements. Although these larvae show considerable between‐brood differences in elemental concentrations for females taken at the same site, there was significant between‐site discrimination of natal signatures for regions only tens of kilometers apart in the waters off of Santa Barbara, California. For several (but not all) elements, differences between regions were consistent between 2 yr. We also explore three different possible proxies (edges of otoliths of adult fishes, resin‐based elemental accumulators, and samples of seawater) that might be used to predict geographic differences in natal signatures. Although these proxies all showed significant regional differences in the concentration of some elements, only manganese showed some congruency in the spatial patterns seen in the larval otoliths. Consequently, currently available proxy measures cannot accurately predict the elemental composition of otolith cores.
Bone mineralisation and strength in range cattle

Cattle (358) from western New South Wales were sampled at abattoirs as part of a survey of mineral status of range cattle. Each animal was described for breed, sex, age, and body condition, and their origin traced back to their range, which was described for forage offered and soil type. Rib bone samples were taken for chemical and mechanical analyses to provide data on percentage phosphorus (% P) and percentage calcium (% Ca) (fat-free bone), percentage ash, ash density, matrix density, ash : matrix, bending moment, and deformation. A tree-based classification model was used to form groups of animals with common background factors (e.g. soil, age, sex, weight). Several of these groups were suspected of being osteodystrophic based on the chemical and physical data. Young cows and cattle in poor body fat condition on poor quality forage were at risk and should have responded to phosphorus supplementation with rain and better pasture conditions. Identification of osteodystrophy in these cattle was most readily diagnosed from ash density data and not from % P, % Ca, or Ca : P. Bone strength interpretation was limited to young cattle. Reference values, as an indication of normal range, are provided for each of the parameters.
Shade signals alter the expression of circadian clock genes in newly‐formed bioenergy sorghum internodes

Abstract Stem internodes of bioenergy sorghum inbred R.07020 are longer at high plant density (shade) than at low plant density (control). Initially, the youngest newly‐formed subapical stem internodes of shade‐treated and control plants are comparable in length. However, full‐length internodes of shade‐treated plants are three times longer than the internodes of the control plants. To identify the early molecular events associated with internode elongation in response to shade, we analyzed the transcriptome of the newly‐formed internodes of shade‐treated and control plants sampled between 4 and 6 hr after the start of the light period (14 hr light/10 hr dark). Sorghum genes homologous to the Arabidopsis shade marker genes ATHB2 and PIL1 were not differentially expressed. The results indicate that shade signals promote internode elongation indirectly because sorghum internodes are not illuminated and grow while enclosed with leaf sheaths. Sorghum genes homologous to the Arabidopsis morning‐phased circadian clock genes LHY, RVE, and LNK were downregulated and evening‐phased genes such as TOC1, PRR5, and GI were upregulated in young internodes in response to shade. We hypothesize that a change in the function or patterns of expression of the circadian clock genes is the earliest molecular event associated with internode elongation in response to shade in bioenergy sorghum. Increased expression of CycD1, which promotes cell division, and decreased expression of cell wall‐loosening and MBF1‐like genes, which promote cell expansion, suggest that shade signals promote internode elongation in bioenergy sorghum in part through increasing cell number by delaying transition from cell division to cell expansion.
Characterization of Triple-Negative Breast Cancer MDA-MB-231 Cell Spheroid Model

Background The tumor three-dimensional (3D) spheroid model in vitro is effective on detecting malignant cells and tumorigenesis, and assessing drug resistance. Compared with two-dimensional (2D) monolayer culture, breast cancer (BC) spheroids more accurately reﬂect the complex microenvironment in vivo, which have been extensively reported in BC research. MDA-MB-231 cells, the triple-negative breast cancer (TNBC) cell line, display representative epithelial to mesenchymal transition (EMT) associated with BC metastasis. However, the characterization of MDA-MB-231 spheroids has been largely unknown at present, which requires further attention. Materials and Methods Microwell array was conducted for the formation of MDA-MB-231 spheroids. In addition, H&E staining, immunohistochemistry (IHC), CellTiter-Glo® 3D cell viability assay, and flow cytometry were performed to investigate the structure and growth characteristics. Besides, Transwell and scratch healing assays were carried out to detect the migratory capacities compared with 2D culture. Western blotting and confocal fluorescence were selected to detect the expression of EMT-associated proteins. Additionally, the half maximal inhibitory concentration (IC50) values of antitumor compounds Carboplatin and Doxorubicin were measured to assess drug resistance. Results The MDA-MB-231 spheroids were viable, which maintained a compact structure with zonation features for up to 9 days. Moreover, those spheroids had a slower growth rate than those cultured as a monolayer and differential zones of proliferation. The migratory capacities were significantly enhanced by transferring the spheroids to 2D adherent culture. Compared with 2D culture, the levels of EMT-associated proteins were significantly up-regulated in spheroids. Furthermore, toxicity assessment showed that spheroids exhibited an increased resistance to the antitumor compounds. Conclusion This study develops the simple spheroids and demonstrates their structure, growth and proliferation characteristics. According to our results, the spheroids are associated with superior EMT and high resistance to toxicological response compared with the standard 2D monocultures.
Seed dispersal in a polder after partial tidal restoration: Implications for salt-marsh restoration

ABSTRACT Question: The vegetation in a polder after partial tidal restoration does not resemble the targeted salt-marsh vegetation. Is this difference in vegetation due to lack of dispersal or unsuitable abiotic conditions ? What could be done for a better restoration of the site? Location: Northwestern France. Methods: Seeds were trapped at the single inlet of the polder with a 200-μm mesh net to estimate inputs of seeds from the bay. In parallel, seed dispersal was studied in the polder by placing Astroturf® seed traps on the surface of the sediment at three different elevations in three distinct areas. Abiotic conditions such as flooding frequency, water table level and soil salinity were monitored. Results: All but one species from the adjacent salt marshes were trapped at the inlet. Not all of these species were on the seed traps inside the polder. Seed dispersal was not homogeneous in the polder and seed trap content mostly discriminated in function of their elevation. Salinity and water logging at the bottom of the slope were very high compared to tolerance of most halophytes but decreased rapidly higher up the slope. Conclusions: The development of salt marsh target species is highly restricted by limited hydrochory inside the polder but also by unfavourable soil conditions induced by the actual hydrological regime. Halophytes are excluded at the bottom of the slope by abiotic conditions and out-competed by subhalophytes higher up. In order to restore salt marsh vegetation inside the polder, a larger opening should be induced in order to increase the flooded surface, and diminish water logging and flooding frequencies.
What Are the Optimal Levels of Time Perspectives? Deviation from the Balanced Time Perspective-Revisited (DBTP-r)

Balanced time perspective (BTP) describes a tendency to focus on past, present and future time horizons that fosters well-being and positive life outcomes. Deviation from the balanced time perspective is a widespread method to measure the balance, but it makes assumptions regarding levels of time perspectives constituting BTP. In the present research we aimed to test the assumptions regarding levels of time perspectives constituting BTP by testing associations between time perspectives and domains of well-being in four independent samples (N = 1150). The results showed that higher well-being was fostered by greater past positive (PP) and future (F) and lower past negative (PN) and present fatalistic (PF) time perspectives in a linear manner. As for the present hedonistic (PH) perspective, the results were inconsistent indicating that this time orientation can be unrelated to well-being or related in an inverse U-shape manner. In the light of our results the optimal values for the deviation from the balanced time perspective, as measured with the Zimbardo Time Perspective Inventory, should be revisited and changed into PN 1, PP 5, PF 1, PH 3.4, F 5, with careful consideration whether or not to incorporate PH into the formula for the deviation from the balanced time perspective at all. We also showed that the deviation from the balanced time perspective using the above values better predicts well-being than the one using previously assumed levels.
Simultaneous genotyping for all three known structural mutations in the human mannose‐binding lectin gene

We describe a rapid and simple method for genotyping the three known structural mutations within exon 1 of the mannan‐binding lectin (MBL) gene. A PCR‐amplifiable synthetic DNA (Universal Heteroduplex Generator) was annealed to genomic PCR product from exon 1 to generate unique DNA heteroduplexes for each mutation. Heteroduplexes were then resolved by non‐denaturing polyacrylamide gel electrophoresis. The technique was initially validated with previously typed samples and then applied to previously untyped samples with the results confirmed by DNA sequencing. © 1997 Wiley‐Liss, Inc.
Feeding, growth, and survival of post-larval abalone Haliotis asinina on different benthic diatoms

The feeding behavior, digestive efficiency, growth, and survival of post-larval abalone Haliotis asinina fed with 5 species of locally isolated benthic diatom strains ( Navicula mollis , N. ramosissima , Stauroneis sp., Pleurosigma sp., and Cocconeis sp.) were examined in the laboratory. Two 15-day feeding trials using 1 mm post-larvae were conducted. No significant differences were observed in sizes of post-larval abalone after 15 days in all diatom treatments ( P >0.05). However, in both trials, Cocconeis sp. resulted in high survival rates (88.9±5.6% and 80.0±20.0% for Trials 1 and 2, respectively). Cocconeis sp. was efficiently digested by post-larval abalone, with most of the cells being ruptured during ingestion and/or passage through the gut. One diatom strain, Pleurosigma sp. , resulted to a high survival but produced the slowest growth rate ( -1 SL). It was probably not ingested easily during the experiment due to its large size or mobility. For the other diatom strains, N. mollis and N. ramosissima , most cells passed through the gut with the cells left intact. Stauroneis sp. is highly digestible, but did not result to high survival, although the remaining live post-larval abalone fed on this diatom as well as on N. mollis grew faster during the second week of both feeding trials. N. ramosissima resulted to poorest survival rate ( Cocconeis sp. showed a fairly high growth rate, digestion efficiency, and survival rate. N. mollis which gave a fairly high survival rate and Stauroneis may be added towards the later stages of post-larval rearing as well as other large diatoms. The digestion efficiency of diatom strains is considered an important factor determining its dietary value, but other factors may also be important such as volume contents, biochemical composition, and other physical characteristics.
Knockdown of TRIM37 Promotes Apoptosis and Suppresses Tumor Growth in Gastric Cancer by Inactivation of the ERK1/2 Pathway

Objective Gastric cancer (GC), a malignant tumor of the gastric mucosa, is the second leading cause of cancer deaths worldwide. Although the incidence and mortality of gastric cancer have been reduced in the US and elsewhere, it is still a major public health concern. In this study, we attempted to investigate the function of tripartite motif-containing protein 37 (TRIM37) in GC cell lines in order to propose a new therapy for GC. Methods The expression of TRIM37 in GC patients and cell lines was detected by immunohistochemistry, real-time PCR and Western blotting analysis. After TRIM37 knockdown or overexpression, the cell cycle, proliferation and apoptosis, as well as the expression of related proteins, were detected. In addition, in vivo experiments on nude mice were performed. Results We found that TRIM37 expression was significantly elevated in tumor tissues of GC patients and GC cell lines, and patients with high expression of TRIM37 had a poor prognosis. Knockdown of TRIM37 in GC cells significantly inhibited cell proliferation and cell cycle progression, promoted apoptosis, increased cleaved caspase 3 and decreased c-myc and phosphorylation of protein kinase 1/2 (p-ERK1/2). Effects of TRIM37 overexpression were opposite to that of TRIM37 knockdown and were potently attenuated by an ERK1/2 inhibitor. In addition, an ERK1/2 agonist increased TRIM37 and p-ERK1/2 in a dose-dependent manner, and TRIM37 knockdown potently attenuated EGF-induced cell proliferation and expression of TRIM37 and p-ERK1/2. Interestingly, we found that TRIM37 overexpression did not affect the mRNA level of dual-specificity phosphatase 6 (DUSP6), but reduced its protein level in GC cells. Co-immunoprecipitation (Co-IP) analyses revealed that TRIM37 interacted with DUSP6, and TRIM37 overexpression enhanced DUSP6 ubiquitination in GC cells. In vivo experiments on nude mice showed the inhibitory effect of TRIM37 knockdown on tumor growth. Conclusion These findings suggest that TRIM37 may act as an oncogene in the growth of GC cells and illustrate its potential function as a target in the treatment of GC.
Ipilimumab and Nivolumab as First-Line Treatment of Patients with Renal Cell Carcinoma: The Evidence to Date

Abstract Immunotherapy has revolutionized the management of metastatic renal cell carcinoma with four checkpoint inhibitors (nivolumab, ipilimumab, avelumab, and pembrolizumab) approved either as monotherapy or as combination therapy. The use of ipilimumab and nivolumab for treatment-naïve, intermediate to poor risk, metastatic renal cell carcinoma was the first checkpoint inhibitor-based combination therapy and remains the only dual checkpoint inhibitor combination approved in mRCC. In this article, we review the trials that led to the approval of ipilimumab and nivolumab in this setting. We also highlight the ongoing trials using this combination, its use in special populations, and clinically relevant unanswered questions.
A world key to Stirtonia (Arthoniaceae), with three new Stirtonia species and one new Crypthonia species from the Neotropics

Abstract A world key to the 21 species of Stirtonia is presented. Three new Stirtonia species are described from the Neotropics: Stirtonia ibirapuitensis Aptroot, Käffer & S. M. Martins, with whitish to cream amoeboid ascigerous areas with lichexanthone on a greenish thallus without lichexanthone and ascospores of 27–32×9·5–12·5 µm; Stirtonia punctiformis Aptroot & Sipman, with ascigerous structures of thallus colour, consisting of one or more brown asci with brown walls with surrounding tissue, in groups or irregular lines and brown ascospores 61–73×27–35 µm; and Stirtonia viridis Aptroot, L. I. Ferraro, Sipman & M. Cáceres, with ascigerous structures mostly linear, branched and anastomosing, whitish, and contrasting with the often greenish thallus and with ascospores 50–58×15–22 µm. In addition, a specimen of S. neotropica is reported that contains some patches of lichexanthone, S. curvata is reported new to the Neotropics from Brazil and the Netherlands Antilles, and S. nivea is reported new to the Northern Hemisphere from Puerto Rico. Also, Crypthonia divaricatica Aptroot & Sipman, with an irregular, thick thallus with divaricatic and usnic acids and flat white ascigerous areas and macrocephalic 5–9-septate ascospores 20–27×9·5–12·5 µm is described from Mexico. While only one Stirtonia species was known from the Neotropics as recently as 2009, the total number of Stirtonia species known from the Neotropics is now 12, an equal number to the 12 species that are known from the Palaeotropics.