Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and Use of a Real-Time Quantitative PCR Method for Detecting and Quantifying Equol-Producing Bacteria in Human Faecal Samples and Slurry Cultures

This work introduces a novel real-time quantitative PCR (qPCR) protocol for detecting and quantifying equol-producing bacteria. To this end, two sets of primers targeting the dihydrodaidzein reductase (ddr) and tetrahydrodaidzein reductase (tdr) genes, which are involved in the synthesis of equol, were designed. The primers showed high specificity and sensitivity when used to examine DNA from control bacteria, such as Slackia isoflavoniconvertens, Slackia equolifaciens, Asaccharobacter celatus, Adlercreutzia equolifaciens, and Enterorhabdus mucosicola. To demonstrate the validity and reliability of the protocol, it was used to detect and quantify equol-producing bacteria in human faecal samples and their derived slurry cultures. These samples were provided by 18 menopausal women under treatment of menopause symptoms with a soy isoflavone concentrate, among whom three were known to be equol-producers given the prior detection of the molecule in their urine. The tdr gene was detected in the faeces of all these equol-producing women at about 4–5 log10 copies per gram of faeces. In contrast, the ddr gene was only amplified in the faecal samples of two of these three women, suggesting the presence in the non-amplified sample of reductase genes unrelated to those known to be involved in equol formation and used for primer design in this study. When tdr and ddr were present in the same sample, similar copy numbers of the two genes were recorded. However, no significant increase in the copy number of equol-related genes along isoflavone treatment was observed. Surprisingly, positive amplification for both tdr and ddr genes was obtained in faecal samples and derived slurry cultures from two non-equol producing women, suggesting the genes could be non-functional or the daidzein metabolized to other compounds in samples from these two women. This novel qPCR tool provides a technique for monitoring gut microbes that produce equol in humans. Monitoring equol-producing bacteria in the human gut could provide a means of evaluating strategies aimed at increasing the endogenous formation of this bioactive compound.
Are Directed Evolution Approaches Efficient in Exploring Nature’s Potential to Stabilize a Lipase in Organic Cosolvents?

Despite the significant advances in the field of protein engineering, general design principles to improve organic cosolvent resistance of enzymes still remain undiscovered. Previous studies drew conclusions to engineer enzymes for their use in water-miscible organic solvents based on few amino acid substitutions. In this study, we conduct a comparison of a Bacillus subtilis lipase A (BSLA) library—covering the full natural diversity of single amino acid substitutions at all 181 positions of BSLA—with three state of the art random mutagenesis methods: error-prone PCR (epPCR) with low and high mutagenesis frequency (epPCR-low and high) as well as a transversion-enriched Sequence Saturation Mutagenesis (SeSaM-Tv P/P) method. Libraries were searched for amino acid substitutions that increase the enzyme’s resistance to the water-miscible organic cosolvents 1,4-dioxane (DOX), 2,2,2-trifluoroethanol (TFE), and dimethyl sulfoxide (DMSO). Our analysis revealed that 5%–11% of all possible single substitutions (BSLA site-saturation mutagenesis (SSM) library) contribute to improved cosolvent resistance. However, only a fraction of these substitutions (7%–12%) could be detected in the three random mutagenesis libraries. To our knowledge, this is the first study that quantifies the capability of these diversity generation methods generally employed in directed evolution campaigns and compares them to the entire natural diversity with a single substitution. Additionally, the investigation of the BSLA SSM library revealed only few common beneficial substitutions for all three cosolvents as well as the importance of introducing surface charges for organic cosolvent resistance—most likely due to a stronger attraction of water molecules.
Nonuniform distribution of collagen density in human knee ligaments

It is generally recognized that the mechanical properties of soft connective tissues are affected by their structural components. We documented collagen density distributions in human knee ligaments to quantify differences in density within and between these ligaments. In order to explain the variations in mechanical properties within and between different knee ligaments as described in the literature, the distributions of collagen density were correlated with these biomechanical findings. Human knee ligaments were shown to be nonhomogeneous structures with regard to collagen density. The anterior bundles of all ligaments contained significantly more collagen mass per unit of volume than the posterior bundles did. The percentage differences between the anterior and posterior bundles, in relation to the posterior bundles, were about 25% for the anterior cruciate ligament (ACL) and the collateral ligaments and about 10% for the posterior cruciate ligament (PCL). Along the cruciate ligaments, the central segments had higher collagen densities than did segments adjacent to the ligament insertions (ACL 9%, PCL 24%). The collagen density in the ACL was significantly lower than that in the other ligaments. These variations within and between the ligaments correlate well with the variations in mechanical properties described in the literature; however, other structural differences have to be taken into account to fully explain the variations in mechanical properties from the structural components.
Bacillus subtilis CtaA and CtaB function in haem A biosynthesis

Haem A, a prosthetic group of many respiratory oxidases, is probably synthesized from haem B (protohaem IX) in a pathway in which haem O is an intermediate. Possible roles of the Bacillus subtilis ctaA and CtaB gene products in haem O and haem A synthesis were studied. Escherichia coli does not contain haem A. The CtaA gene on plasmids in E. coli resulted in haem A accumulation in membranes. The presence of CtaB together with ctaA increased the amount of haem A found in E. coli. Haem O was not detected in wild‐type B. subtilis strains. A previously isolated B. subtilis CtaA deletion mutant was found to contain haem B and haem O, but not haem A. B. subtilis ctaB deletion mutants were constructed and found to tack both haem A and haem O. The results with E. coli and B. subtilis strongly suggest that the B. subtilis CtaA protein functions in haem A synthesis. It is tentatively suggested that it functions in the oxygeNatlon/oxidation of the methyl side group of carbon 8 of haem O. B. subtilis CtaB, which is homologous to Saccharomyces cerevisiae COX10 and E. coli CyoE, also has a role in haem A synthesis and seems to be required for both cytochrome a and cytochrome o synthesis.
Identification of reptilian genes encoding hair keratin-like proteins suggests a new scenario for the evolutionary origin of hair

The appearance of hair is one of the main evolutionary innovations in the amniote lineage leading to mammals. The main components of mammalian hair are cysteine-rich type I and type II keratins, also known as hard α-keratins or “hair keratins. ” To determine the evolutionary history of these important structural proteins, we compared the genomic loci of the human hair keratin genes with the homologous loci of the chicken and of the green anole lizard Anolis carolinenis. The genome of the chicken contained one type II hair keratin-like gene, and the lizard genome contained two type I and four type II hair keratin-like genes. Orthology of the latter genes and mammalian hair keratins was supported by gene locus synteny, conserved exon–intron organization, and amino acid sequence similarity of the encoded proteins. The lizard hair keratin-like genes were expressed most strongly in the digits, indicating a role in claw formation. In addition, we identified a novel group of reptilian cysteine-rich type I keratins that lack homologues in mammals. Our data show that cysteine-rich α-keratins are not restricted to mammals and suggest that the evolution of mammalian hair involved the co-option of pre-existing structural proteins.
Gaussian synapse ANNs in multi- and hyperspectral image data analysis

A new type of artificial neural network is used to identify different crops and ground elements from hyperspectral remote sensing data sets. These networks incorporate Gaussian synapses and are trained using a specific algorithm called Gaussian synapse back propagation described here. Gaussian synapses present an intrinsic filtering ability that permit concentrating on what is relevant in the spectra and automatically discard what is not. The networks are structurally adapted to the problem complexity as superfluous synapses and/or nodes are implicitly eliminated by the training procedure, thus pruning the network to the required size straight from the training set. The fundamental difference between the present proposal and other ANN topologies using Gaussian functions is that the latter use these functions as activation functions in the nodes, while in our case, they are used as synaptic elements, allowing them to be easily shaped during the training process to produce any type of n-dimensional discriminator. This paper proposes a multi- and hyperspectral image segmenter that results from the parallel and concurrent application of several of these networks providing a probability vector that is processed by a decision module. Depending on the criteria used for the decision module, different perspectives of the same image may be obtained. The resulting structure offers the possibility of resolving mixtures, that is, carrying out a spectral unmixing process in a very straightforward manner.
Plains Prickly Pear Response to Fire: Effects of Fuel Load, Heat, Fire Weather, and Donor Site Soil

Abstract Plains prickly pear (Opuntia polyacantha Haw.) is common throughout the Great Plains and often becomes detrimental to agricultural production on noncultivated lands. We examined direct fire effects on plains prickly pear and mechanisms of tissue damage to facilitate development of fire prescriptions. Cladodes from clones on three soils (claypan, gravelly, silty) were subjected to fire with two weather conditions (moderate, severe) at four fuel loads (1 500, 3 000, 4 500, and 6 000 kg · ha−1) and a nonburned control. Fire was simulated with field-collected grass, and heat was measured using thermocouples at the soil surface and 8 cm above. Plants were maintained in a greenhouse and monitored for cladode mortality or growth. Cactus response to fire was examined in a field experiment with four nonburned and four summer-burned 0.75-ha plots. Some plants from each treatment sprouted new cladodes. Donor site soil and fire weather effects were limited to mass of new sprouts as they interacted with fuel load. Fire under any condition reduced cactus mass and survival. Reduction in cactus mass increased from 42% with 1 500 kg · ha−1 to 92% with fuel loads of 3 000 kg · ha−1 or more. Fuel load, duration of heat, maximum temperature, and degree-seconds were each positively related to mortality, but duration of heat greater than 60°C was the best predictor. Plant mortality was 15% in the field, but number of live cladodes was initially reduced 91%. After one year, number of live cladodes in burned plots was 43% of that in nonburned plots because burned plants sprouted more new cladodes than nonburned plants. Insect and browsing damage occurred on 83% of cladodes in burned plots and only 8% for nonburned plots. Lack of fire weather effects suggests prickly pear control can be achieved under broad fire prescriptions, given the amount of combustible fuel is adequate.
What is satisfying about satisfying events? Testing 10 candidate psychological needs.

Three studies compared 10 candidate psychological needs in an attempt to determine which are truly most fundamental for humans. Participants described "most satisfying events" within their lives and then rated the salience of each of the 10 candidate needs within these events. Supporting self-determination theory postulates (Ryan & Deci, 2000)--autonomy, competence, and relatedness, were consistently among the top 4 needs, in terms of both their salience and their association with event-related affect. Self-esteem was also important, whereas self-actualization or meaning, physical thriving, popularity or influence, and money-luxury were less important. This basic pattern emerged within three different time frames and within both U.S. and South Korean samples and also within a final study that asked, "What's unsatisfying about unsatisfying events? " Implications for hierarchical theories of needs are discussed.
Clinical and Imaging Characteristics of Orbital Leukemic Tumors

Purpose: To characterize the clinical and imaging features of orbital leukemic tumors in 27 patients seen and treated at St. Jude Children's Research Hospital. Methods: A retrospective review was performed on the clinical and imaging records of 27 consecutive patients with a diagnosis of orbital leukemic tumors. The following data were extracted from the patients' records: age at diagnosis of orbital leukemic tumors, sex, race, national origin, type of leukemia, temporal relationship of orbital disease to diagnosis of leukemia, survival from diagnosis of orbital leukemic tumor, laterality of the orbital disease, location of the mass within the orbit, imaging features of the mass, chemotherapeutic protocol, treatment with bone marrow transplant, and orbital radiation. Results: The median age at diagnosis of orbital leukemic tumor was 8 years (range, 1–18 years). Nineteen of the 27 patients were male, and 21 patients were born and lived in the United States. Twenty-one patients had acute myeloid leukemia, five had acute lymphoblastic leukemia, and one had chronic myelogenous leukemia. In 85% of patients (n = 23), the diagnosis of leukemia was based on the bone marrow examination findings. Orbital imaging revealed homogenous masses that molded to one or more orbital walls without bony destruction. Nine patients had bilateral orbital involvement. All patients received multiagent systemic chemotherapy, and 14 underwent bone marrow transplantation. Five patients received external beam radiation for the treatment of orbital disease. Fifteen (55.6%) of the 27 patients were alive at the time of the study. The median survival for all patients was 4.75 years (range, 0.1–24 years) after the diagnosis of orbital disease. Conclusions: Orbital leukemic tumors occur most commonly in the first decade of life, in association with acute myeloid leukemia. They appear as homogenous masses along the orbital walls. Although the overall survival rate for patients with leukemia has improved over the past 3 decades, the mortality of patients who develop orbital leukemic tumors remains high.
Dual regulation of the AMP‐activated protein kinase provides a novel mechanism for the control of creatine kinase in skeletal muscle

The AMP‐activated protein kinase (AMPK) is activated by a fall in the ATP:AMP ratio within the cell in response to metabolic stresses. Once activated, it phosphorylates and inhibits key enzymes in energy‐consuming biosynthetic pathways, thereby conserving cellular ATP. The creatine kinase–phosphocreatine system plays a key role in the control of ATP levels in tissues that have a high and rapidly fluctuating energy requirement. In this study, we provide direct evidence that these two energy‐regulating systems are linked in skeletal muscle. We show that the AMPK inhibits creatine kinase by phosphorylation in vitro and in differentiated muscle cells. AMPK is itself regulated by a novel mechanism involving phosphocreatine, creatine and pH. Our findings provide an explanation for the high expression, yet apparently low activity, of AMPK in skeletal muscle, and reveal a potential mechanism for the co‐ordinated regulation of energy metabolism in this tissue. Previous evidence suggests that AMPK activates fatty acid oxidation, which provides a source of ATP, following continued muscle contraction. The novel regulation of AMPK described here provides a mechanism by which energy supply can meet energy demand following the utilization of the immediate energy reserve provided by the creatine kinase–phosphocreatine system.
An examination of long-term abnormal stock returns following stock dividends

With 185 months Chinese capital market data, this paper proves that the Fama-French Three-Factor Model has an excellent explanation on the cross-sectional variation in average stock returns. Furthermore, the examination of long-term abnormal stock returns following stock dividends based on the three-factor model and zero-investment portfolio model shows that the corporations which have stock dividends suffered a lower returns compared to their matched firms which don't have the same company event. The results suggest that the long-term investment on such firms is not beneficial, which is a negative evidence of the signaling hypothesis.
Short communication Isolation and characterisation of Shiga toxin-producing Escherichia coli O157:H7 from calves in Argentina

Four hundred and twenty-two calves were examined for intestinal carriage of Shiga toxin-producing Escherichia coli O157:H7 using conventional plating. Two (0.5%) E. coli O157 were recovered. They were compared with 96 Argentine strains of different origin by pulsed-field gel electrophoresis,phage typing and PCR-RFLP of stx2 genes. One strain isolated from a calf,was closely related with 18 strains of clinical origin. 2003 Elsevier Science Ltd. All rights reserved.
Endogenous testosterone, endothelial dysfunction, and cardiovascular events in men with nondialysis chronic kidney disease.

BACKGROUND AND OBJECTIVES Deterioration of kidney function impairs testosterone production, with hypogonadism being common in men with chronic kidney disease (CKD). In nonrenal populations, testosterone is suggested to participate in the atherosclerotic process. In male dialysis patients, we showed that low testosterone increases the risk of mortality. We here studied plausible links among testosterone levels, vascular derangements, and cardiovascular events in nondialysis CKD men. DESIGN, SETTING, PARTICIPANTS, & METHODS This was a cross-sectional analysis in which flow-mediated dilation (FMD) was assessed in 239 CKD male patients (stages 1 to 5; mean age 52 ± 12 years), together with routine measurements, serum total and free testosterone, and follow-up for cardiovascular outcomes. RESULTS Total and free testosterone levels decreased in parallel with the reduction of kidney function. Multiple regression analyses showed that total and free testosterone significantly and independently contributed to explain the variance of FMD. After a median follow-up of 31 months (range 8 to 35 months), 22 fatal and 50 nonfatal cardiovascular events occurred. In Cox analysis, the risk of cardiovascular events was reduced by 22% for each nanomole-per-liter increment of total testosterone. This reduced risk persisted after adjustment for age, renal function, diabetes mellitus, previous cardiovascular history, C-reactive protein, albumin, and FMD. The same was true for free testosterone concentrations. CONCLUSIONS The reduction in endogenous testosterone levels observed with progressive CKD was inversely associated with endothelial dysfunction and exacerbated the risk of future cardiovascular events in nondialysis male CKD patients.
Comparing vaginal and sublingual administration of misoprostol for labour induction in women with intra-uterine fetal death

The objective of this study was to compare complications and effectiveness of induction after vaginal and sublingual administration of misoprostol for labor induction in women with intra-uterine fetal death (IUFD). In a district hospital in Ghana, 23 women with IUFD who underwent labor induction with sublingual misoprostol were compared with a control group of 21 women who received vaginal misoprostol. In the vaginal group 28.6% had one or more complications compared to 21.7% in the sublingual group. In the sublingual group three inductions did not lead to delivery within 48 hours (13%), compared to four in the other group (19%). The mean induction-to-delivery time in the sublingual group was 13 hours and 17 hours in the vaginal group. In this study, both sublingual and vaginal misoprostol were safe and efficient for labor induction in women with IUFD. However, more research on larger numbers of patients is needed, in order to compare complications.
Shock-Sensitivity in Shell-Like Structures: With Simulations of Spherical Shell Buckling

Under increasing compression, an unbuckled shell is in a metastable state which becomes increasingly precarious as the buckling load is approached. So to induce premature buckling, a lateral disturbance will have to overcome a decreasing energy barrier which reaches zero at buckling. Two archetypal problems that exhibit a severe form of this behavior are the axially-compressed cylindrical shell and the externally pressurized spherical shell. Focusing on the cylinder, a nondestructive technique was recently proposed to estimate the “shock-sensitivity” of a laboratory specimen using a lateral probe to measure the nonlinear load-deflection characteristic. If a symmetry-breaking bifurcation is encountered on the path, computer simulations showed how this can be suppressed by a controlled secondary probe. Here, we extend our understanding by assessing in general terms how a single control can capture remote saddle solutions: in particular, how a symmetric probe could locate an asymmetric solution. Then, more s.
The Impact of Serum Interleukin-17 on Chronic Hepatitis C and Its

Background: Recently, interleukin-17 (IL-17) cytokine family plays important roles in the host immunity in chronic inflammatory conditions, autoimmune and viral liver diseases. However, studies on the IL-17 role in the immunopathogenesis of hepatitis C virus (HCV) infection are limited. Objectives: to assess serum IL-17 levels in chronically HCV infected patients and their relations to the severity of liver disease. Patients and methods: The study included 200 chronically HCV infected patients; 100 chronic hepatitis C, 100 liver cirrhosis including 35 with hepatocellular carcinoma (HCC) and 30 controls. Serum IL-17 levels were quantified by ELISA. Results: Serum IL-17 levels were significantly higher in chronically HCV infected patients than controls and cirrhotics had the highest levels (P<0.001). These levels were positively related with inflammation grade and fibrosis stage. Serum IL-17 was significantly higher in HCC than controls. IL-17 was significantly correlated with prothrombin time, ALT, serum albumin, viral load, and alpha fetoprotein-L3. Conclusion: IL-17 levels were increased with increasing liver disease progression and chronicity. Thus, IL-17 may be an important biological marker for the immunopathogenesis of chronic hepatitis, liver fibrosis and HCC.