Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarray-Based Transcriptome Analysis of Recombinant Pichia Pastoris Strains Overexpressing Alpha-Amylase and Interleukin-2

DNA microarray has been a useful tool for global-scale transcriptome analysis. To study the cellular response to expression of recombinant proteins, we compared the transcriptional profiles of recombinant Pichia pastoris strains overexpressing amylase and interleukin-2 versus that of the control strain at different cellular states. The microarray analysis was carried out via the use of Yeast_2 array specific for Saccharomyces cerevisiae and Schizosaccharomyces pombe. The transcirptome analysis of each studied strain at logarithmic growth phase and stationary growth phase showed hundreds of significant differences. In contrast, in comparison of studied strains at the same time points, the numbers of gene which are differentially expressed is rather low. Interestingly, the expression of heterologous alpha-factor secretion signal in the strains overexpressing amylase and interleukin-2 was up-regulated by more than 15 times and 140 times at the exponential and stationary phase, respectively. The results also provide evidence about the false positive result in microarray data when using non-specific array.
In vitro ileal and caecal fermentation of fibre substrates in the growing pig given a human-type diet

Abstract This study characterised the in vitro ileal fermentability of different substrates in the growing pig, adopted as an animal model for the adult human, and compared in vitro ileal and caecal fermentation in the pig. Substrates (arabinogalactan (AG), cellulose, fructo-oligosaccharide (FOS), inulin, mucin, citrus pectin and resistant starch) were fermented in vitro (ileal 2 h and caecal 24 h) with an ileal or caecal inoculum prepared from ileal or caecal digesta collected from growing pigs (n 5) fed a human-type diet for 15 d. The organic matter (OM) fermentability and production of organic acids were determined. In general, there was considerable in vitro ileal fermentation of fibre, and the substrates differed (P < 0·001) for both in vitro ileal and caecal OM fermentability and for organic acid production. Pectin had the greatest in vitro ileal OM fermentability (26 %) followed by AG, FOS and resistant starch (15 % on average), and cellulose, inulin and mucin (3 % on average). The fermentation of FOS, inulin and mucin was greater for in vitro caecal fermentation compared with the ileal counterpart (P ≤ 0·05). In general, the organic acid production was higher for in vitro caecal fermentation (P ≤ 0·05). For instance, the in vitro ileal acetic acid production represented 4–46 % of in vitro caecal production. Energy from fibre fermentation of 0·6–11 kJ/g substrate fermented could be expected in the ileum of the pig. In conclusion, substrates are fermented in both the ileum and caecum. The degree of fermentation varies among substrates, especially for in vitro ileal fermentation.
Extracellular polymer substances and the heterogeneity of Clostridium acetobutylicum biofilm induced tolerance to acetic acid and butanol

The mechanisms associated with how cells in biofilms exhibit enhanced tolerance to adverse environmental stress have attracted much recent attention. In this study, we investigated the tolerance mechanisms through observation of biofilm morphology combined with detection of fermentation activity, and discovered an improved way to culture biofilms for application in acetone–butanol–ethanol (ABE) fermentation. We found that a mature biofilm exhibited enhanced tolerance to acetic acid and butanol during ABE fermentation. A mature biofilm consists of a complex, heterogeneity three-dimensional structure, with a coated extracellular polymer substance (EPS). Therefore, when exposed to a harsh environment, cells in different regions of the biofilm displayed different levels of performance, resulting in cells with higher tolerance levels capable of survival, continued growth. The EPS acted as a barrier, limiting the transfer of harmful substances, and diluting their concentration in order to protect biofilm cells. During repeated-batch fermentations, the continuous fermentation formed biofilms, and the butanol concentration, productivity, and yield were 22.08%, 26.37%, and 61.08% higher, respectively, relative to suspended fermentation.
Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane

Significance The proto-oncogene KRAS, a small GTPase, is frequently mutated in pancreatic, colorectal, and lung cancer. These mutations result in elevated levels of the activated guanosine triphosphate-bound form of KRAS. Localized at the plasma membrane, KRAS functions to recruit effectors, predominantly RAF kinase for activation and initiation of the MAPK signaling cascade. Combining computational and biophysical methods we identify a membrane-distal state of the KRAS G-domain that alternates with two previously described membrane-proximal states through dynamic reorganization of the hypervariable region. Comprising about 90% of the ensemble, this membrane-distal state of the G-domain dominates the proximal states and may facilitate KRAS to recruit cytosolic RAF kinase to the membrane by a fly-casting mechanism. The small GTPase KRAS is localized at the plasma membrane where it functions as a molecular switch, coupling extracellular growth factor stimulation to intracellular signaling networks. In this process, KRAS recruits effectors, such as RAF kinase, to the plasma membrane where they are activated by a series of complex molecular steps. Defining the membrane-bound state of KRAS is fundamental to understanding the activation of RAF kinase and in evaluating novel therapeutic opportunities for the inhibition of oncogenic KRAS-mediated signaling. We combined multiple biophysical measurements and computational methodologies to generate a consensus model for authentically processed, membrane-anchored KRAS. In contrast to the two membrane-proximal conformations previously reported, we identify a third significantly populated state using a combination of neutron reflectivity, fast photochemical oxidation of proteins (FPOP), and NMR. In this highly populated state, which we refer to as “membrane-distal” and estimate to comprise ∼90% of the ensemble, the G-domain does not directly contact the membrane but is tethered via its C-terminal hypervariable region and carboxymethylated farnesyl moiety, as shown by FPOP. Subsequent interaction of the RAF1 RAS binding domain with KRAS does not significantly change G-domain configurations on the membrane but affects their relative populations. Overall, our results are consistent with a directional fly-casting mechanism for KRAS, in which the membrane-distal state of the G-domain can effectively recruit RAF kinase from the cytoplasm for activation at the membrane.
Sleep Duration Regularity, But Not Sleep Duration, is Associated with Microvascular Function in College Students.

STUDY OBJECTIVES Vascular dysfunction is a hypothesized mechanism linking poor sleep habits to an increased incidence of cardiovascular diseases. However, the vascular profile associated with free-living sleep duration and sleep regularity has not been well elucidated, particularly in young adults. Thus, this study aimed to evaluate the associations between mean sleep duration, regularity in sleep duration, and peripheral vascular function in young adult college students. METHODS Fifty-one healthy undergraduate students (20±1 years) completed 14 days of 24-hour wrist actigraphy and subsequent vascular assessments. Macrovascular function was measured using brachial artery flow-mediated dilation (FMD) while microvascular function was measured via passive leg movement (PLM). RESULTS Mean sleep duration was unrelated to FMD and PLM. Conversely, more irregular sleep duration (14-day sleep duration standard deviation [SD]) was unfavorably associated with all three measures of PLM-induced hyperemia (peak leg blood flow [LBF], p=0.01; change in LBF from baseline to peak, p<0.01; LBF area under the curve, p<0.01), and remained significant in regression models which adjusted for sex, body mass index, blood pressure, physical activity, alcohol and caffeine consumption, and sleep duration (all p<0.05). When using a median split to dichotomize "low" and "high" sleep duration SD groups, those demonstrating high variability in sleep duration exhibited ~45% lower PLM responses compared to those demonstrating low variability. CONCLUSIONS Irregular sleep duration is associated with poorer microvascular function as early as young adulthood. These findings support the growing body of evidence that irregular sleep patterns may be an independent and modifiable risk factor for cardiovascular disease.
Frontal, Parietal, and Temporal Brain Areas Are Differentially Activated When Disambiguating Potential Objects of Joint Attention

Abstract Humans establish joint attention with others by following the other’s gaze. Previous work has suggested that a cortical patch (gaze-following patch, GFP) close to the posterior superior temporal sulcus (pSTS) may serve as a link between the extraction of the other’s gaze direction and the resulting shifts of attention, mediated by human lateral intraparietal area (hLIP). However, it is not clear how the brain copes with situations in which information on gaze direction alone is insufficient to identify the target object because more than one may lie along the gaze vector. In this fMRI study, we tested human subjects on a paradigm that allowed the identification of a target object based on the integration of the other’s gaze direction and information provided by an auditory cue on the relevant object category. Whereas the GFP activity turned out to be fully determined by the use of gaze direction, activity in hLIP reflected the total information needed to pinpoint the target. Moreover, in an exploratory analysis, we found that a region in the inferior frontal junction (IFJ) was sensitive to the total information on the target. An examination of the BOLD time courses in the three identified areas suggests functionally complementary roles. Although the GFP seems to primarily process directional information stemming from the other’s gaze, the IFJ may help to analyze the scene when gaze direction and auditory information are not sufficient to pinpoint the target. Finally, hLIP integrates both streams of information to shift attention to distinct spatial locations.
Occurrence and Characteristics of Resistant Strains of Corynespora melonis against Benzimidazole Compounds

Corynespora属菌に有効なことからキュウリ褐斑病の防除に使用されたベノミル剤の効力低下が1980年に初めて報告された。 大分県をはじめ九州各地のキュウリ圃場から採取分離した419菌株についてベノミルおよびカルベンダジムに対する感受性を検討したところ,これらの菌株のうち330菌株の最低生育阻止濃度が100μg/ml以上におよび,残りの89菌株のそれは10∼1μg/ml以下であり,低感受性系統と高感受性系統に明確に区別された。 最低生育阻止濃度の頻度分布は2峰型を示し,その中間の濃度域内に最低生育阻止濃度をもつ耐性菌群はまったく認められなかった。 両系統には,キュウリ葉および果実に対する病原力およびPSA培地上での菌糸伸長力や胞子形成力などに差異が認められなかった。 九州地域のキュウリ圃場においてはこの耐性菌がさまざまな割合で混在し,これが防除効果に影響したと考えられた。 1973年以降ベンズイミダゾール系薬剤がキュウリ栽培地帯で広く使用されたため,これらの薬剤耐性菌が発現したものと考えられた。
Maturity Progression of the Entire Anterior Cruciate Ligament Graft of Insertion-Preserved Hamstring Tendons by 5 Years: A Prospective Randomized Controlled Study Based on Magnetic Resonance Imaging Evaluation

Background: It has been reported that insertion-preserved hamstring tendon autografts (IP-HT) have better maturity than free hamstring tendon autografts (FHT) at 2 years after anterior cruciate ligament reconstruction (ACLR); however, whether insertion preservation improves the maturity of the entire autograft and clinical outcomes at 5 years after ACLR is still unclear. Purpose: To investigate the clinical outcomes and maturity of different segments using insertion-preserved and free hamstring tendon autografts up to 5 years after ACLR. Study Design: Randomized controlled trial; Level of evidence, 2. Methods: 45 patients who underwent isolated ACLR with hamstring tendon autografts were enrolled and randomized into 2 groups. The study group had ACLR with IP-HT, whereas the control group had ACLR with FHT. The International Knee Documentation Committee and Tegner scores, Lysholm activity score, and KT-1000 arthrometer measurements were evaluated preoperatively and at 6, 12, 24, and 60 months postoperatively. Three-dimensional-reconstruction MRI examinations were performed at 6, 12, 24, and 60 months to evaluate the signal/noise quotient (SNQ) values of femoral tunnel graft, intra-articular graft, and tibial tunnel graft. Results: At 60 months, the SNQ values of the intra-articular and tunnel sections for the grafts in both groups showed no difference; the clinical outcomes were improved compared with before surgery (P < .001) and were similar in both groups. In the early stage, all graft segments in the IP-HT group had lower SNQ values than those of the FHT group. At 6 months, the entire graft in the FHT group and the femoral tunnel section in the IP-HT group had the maximum SNQ values, whereas the femoral tunnel graft had the highest SNQ value compared with intra-articular and tibial tunnel graft in each group. SNQ values of the intra-articular and tibial tunnel graft in the IP-HT group had no significant change within 60 months. Conclusion: All patients had similar clinical outcomes and graft maturity at 60 months postoperatively. The SNQ values and progressions varied at different graft sites and were highest for the femoral tunnel graft. All significantly changing SNQ values reached the maximum value at 6 months. Compared with FHT autograft, the graft maturity of IP-HT autograft recovered earlier and appeared more stable within the 60-month follow-up; however, no significant association was found between graft maturity and clinical scores.
Psychological Factors Associated with Functional Disability in Patients with Hip and Knee Osteoarthritis

Abstract Several studies have shown an association between psychosocial variables and functional capacity in chronic pain processes such as osteoarthritis. The aim of this study was to test a structural equations model that shows the predictive weight of certain variables such as catastrophizing, self-efficacy and kinesiophobia on functional pain and WOMAC subscales scores of pain and physical function of older patients diagnosed with hip and knee osteoarthritis. We also assessed the specific weight of age in terms of the factors. The study was conducted on a sample of 170 patients (142 women and 28 men mean age, 74.44 years range, 50–96 years). The main variables evaluated were WOMAC subscales scores of pain and physical function, self-efficacy, catastrophizing and kinesiophobia. To assess these variables, we used the Spanish validated version of the Western Ontario and McMaster Universities questionnaire, the Chronic Pain Self-Efficacy Scale, the Pain Catastrophizing Scale and the Tampa Scale for Kinesiophobia, respectively. We tested a structural equations model (IBM SPSS Amos version 22). The results showed the predominant predictive weight (both direct and indirect) of catastrophizing while simultaneously ruling out the relevance of age as a predictor of WOMAC subscales scores of pain and physical function. This study provides data of interest on the explanatory mechanisms that underlie the direct and inverse relationships between the studied psychological variables.
Four new narrow-range endemic species of Gulella from Eastern Cape, South Africa (Mollusca : Pulmonata : Streptaxidae)

Gulella dejae sp. n. , G. hamerae sp. n. , G. latimerae sp. n. and G. newmani sp. n. are described from the Transkei region, Eastern Cape, South Africa. All are unusual amongst southern African Gulella species in having a peristome which is not interrupted in the parietal region, G. latimerae sp. n. and G. newmani sp. n. also being exceptional in having a detached apertural tube. The conservation of the species is discussed in relation both to their restricted ranges and to the vulnerability of forest habitats in which they occur. All appear to meet the criteria for red-listing as threatened species.
CPAP combined with oral appliance therapy reduces CPAP requirements and pharyngeal pressure swings in obstructive sleep apnea.

STUDY OBJECTIVES Oral appliance (OA) therapy is the leading alternative to continuous positive airway pressure (CPAP) for obstructive sleep apnea (OSA). It is well tolerated compared to CPAP. However, ≥50% of patients using OA therapy have incomplete resolution of their OSA. Combination therapy with CPAP and oral appliance (CPAP+OA) is a potential alternative for incomplete responders to OA therapy. This study aimed to determine the extent to which combination therapy reduces therapeutic CPAP requirements using gold standard physiological methodology in those who have an incomplete response to OA therapy alone. METHODS 16 incomplete responders (residual AHI> 10events/h) to a novel OA with a built-in oral airway were recruited (3F:13M, aged 31-65 years, BMI: 22-38kg/m2, residual AHI range 13-63events/h). Participants were fitted with a nasal mask, pneumotachograph, epiglottic pressure catheter and standard polysomnography equipment. CPAP titrations were performed during NREM supine sleep in each participant during 3 conditions (order randomized): 1) CPAP only, 2) CPAP+OA(oral airway open), and 3) CPAP+OA(oral airway closed). RESULTS OSA was resolved at pressures of 4±2 and 5±2cmH2O during CPAP+OA (oral airway open) and CPAP+OA (oral airway closed) conditions versus 8±2cmH2O during CPAP only (P<0.01). Negative epiglottic pressure swings in oral airway open and closed conditions were normalized to CPAP only levels (-2.5[-3.7,-2.6] vs. -2.3[-3.2,-2.4]vs. -2.1[-2.7,-2.3]cmH2O). CONCLUSIONS Combined CPAP and OA therapy reduces therapeutic CPAP requirements by 35-45% and minimizes epiglottic pressure swings. This combination may be a therapeutic alternative for patients with incomplete responses to OA therapy alone and those who cannot tolerate high CPAP levels.
α-Linolenic and γ-linolenic acids exercise differential antitumor effects on HT-29 human colorectal cancer cells.

α-Linolenic acid (ALA, 18:3n-3) and γ-gamma linolenic acid (GLA, 18:3n-6) are polyunsaturated fatty acids (PUFA) that improve the human health. The present study focused on testing the in vitro antitumor actions of pure ALA and GLA on the HT-29 human colorectal cancer cell line. Cell viability was checked by MTT ((3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) test, cell membrane damage by the lactate dehydrogenase assay, apoptosis was tested by both caspase-3 activity trial and transmission electron microscopy images, and protein composition was analyzed by quantitative proteomics analysis. MTT test revealed IC50 values of 230 and 255 μM for ALA and GLA, respectively, at 72 h. After 24 h of incubation, both ALA and GLA induced apoptosis on HT-29 colorectal cancer cells according to the caspase-3 assay and microscopy images. SWATH/MS analysis evidenced that ALA significantly affected the mitochondrial protein import pathway and the citric acid cycle pathway, while GLA did not significantly affect any particular pathway. In summary, both ALA and GLA showed concentration-dependent inhibitory effects on HT-29 cells viability and induced cell death by apoptosis. ALA significantly affected cellular pathways, while GLA does not have specific actions on either pathway. Both n-3 and n-6 C18 PUFA are bioactive food components useful in the colorectal cancer prevention.
A rapid point-of-care ultrasound marker for muscle mass and muscle strength in older adults

Abstract Background/Objectives Sarcopenia is defined as the gradual age-associated loss of both muscle quantity and strength in older adults, and is associated with increased mortality, falls, fractures and hospitalisations. Current sarcopenia criteria use dual-energy X-ray absorptiometry (DXA) measures of muscle mass, a test that cannot be performed at the bedside, unlike point-of-care ultrasound (PoCUS). We examined the association between ultrasonic measures of muscle thickness (MT, vastus medialis muscle thickness) and measures of muscle quantity and strength in older adults. Methods A total of 150 older adults (age ≥ 65; mean age 80.0 ± 0.5 years, 66 women, 84 men) were recruited sequentially from geriatric medicine clinics. Each subject had lean body mass (LBM, by bioimpedance assay), grip strength, mid-arm biceps circumference (MABC), gait speed and MT measured. All initial models were adjusted for biological sex. Results In our final parsimonious models, MT showed a strong significant correlation with all measures of muscle mass, including LBM (Standardised β = 0.204 ± 0.058, R2 = 0.577, P < 0.001) and MABC (Standardised β = 0.141 ± 0.067, R2 = 0.417, P = 0.038). With respect to measures of muscle quality, there was a strong significant correlation with grip strength (Standardised β = 0.118 ± 0.115, R2 = 0.511, P < 0.001) but not with subject performance (gait speed). Conclusions MT showed strong correlations with both measures of muscle mass (LBM and MABC) and with muscle strength (grip strength). Although more work needs to be done, PoCUS shows potential as a screening tool for sarcopenia in older adults.
Germline mutational profile of Chinese patients under 70 years old with colorectal cancer

Inherited susceptibility accounts for nearly one‐third of colorectal cancer (CRC) predispositions and has an 80%‐100% lifetime risk of this disease. However, there are few data about germline mutations of hereditary CRC‐related genes in Chinese patients with CRC. This study aimed to assess the prevalence of gene mutations related to cancer susceptibility among Chinese patients with CRC, differences between Chinese and Western patients, and the phenotype‐genotype correlation.
A Comparative Analysis of Allergen Proteins between Plants and Animals Using Several Computational Tools and Chou’s PseAAC Concept

Background: A large number of allergens are derived from plant and animal proteins. A major challenge for researchers is to study the possible allergenic properties of proteins. The aim of this study was in silico analysis and comparison of several physiochemical and structural features of plant- and animal-derived allergen proteins, as well as classifying these proteins based on Chou’s pseudo-amino acid composition (PseAAC) concept combined with bioinformatics algorithms. Methods: The physiochemical properties and secondary structure of plant and animal allergens were studied. The classification of the sequences was done using the PseAAC concept incorporated with the deep learning algorithm. Conserved motifs of plant and animal proteins were discovered using the MEME tool. B-cell and T-cell epitopes of the proteins were predicted in conserved motifs. Allergenicity and amino acid composition of epitopes were also analyzed via bioinformatics servers. Results: In comparison of physiochemical features of animal and plant allergens, extinction coefficient was different significantly. Secondary structure prediction showed more random coiled structure in plant allergen proteins compared with animal proteins. Classification of proteins based on PseAAC achieved 88.24% accuracy. The amino acid composition study of predicted B- and T-cell epitopes revealed more aliphatic index in plant-derived epitopes. Conclusions: The results indicated that bioinformatics-based studies could be useful in comparing plant and animal allergens.