Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of loss of DNA mismatch repair on development of topotecan-, gemcitabine-, and paclitaxel-resistant variants after exposure to cisplatin.

Loss of DNA mismatch repair (MMR) causes genomic instability by markedly increasing the frequency of sporadic mutations in both coding and noncoding sequences. Little is known about how loss of MMR affects sensitivity to the mutagenic effect of chemotherapeutic agents. We wanted to determine how loss of MMR affects the ability of cisplatin, a known mutagen, to generate human tumor cell variants resistant to other drugs with which cisplatin is commonly combined in treatment regimens. We compared the ability of cisplatin to produce variants resistant to topotecan, gemcitabine, and paclitaxel in two pairs of MMR-proficient and -deficient cells that included sublines of the human colon carcinoma cell line HCT-116 and sublines of the human endometrial adenocarcinoma cell line HEC59. Cells were exposed to increasing concentrations of cisplatin for 1 h, and the surviving population was tested for the frequency of variants resistant to these single molecular target drugs 10 days later. The frequency of variants increased linearly with cisplatin concentration for all three drugs. Cisplatin was 2.6 +/- 0.3- (S.D.), 3.6 +/- 0.9-, and 2.3 +/- 0.1-fold more potent at producing topotecan-, gemcitabine-, and paclitaxel-resistant variants in the MMR-deficient than in the MMR-proficient HCT116 cells (P <.05 for all). Cisplatin was 1.4 +/- 0.3- and 1.4 +/- 0.4-fold more potent at generating topotecan- and gemcitabine-resistant variants in MMR-deficient HEC59 cells than in MMR-proficient HEC59+ch2 cells. Cisplatin was not more potent in generating paclitaxel-resistant variants in the MMR-deficient HEC59 cells. Spontaneous rates of generation of cells resistant to these three drugs were also measured in the HCT116 sublines. MMR-deficient HCT116 cells exhibited rates of generation of resistant variants that were 1.94- and 1.51-fold higher (P <.05) than those in the MMR-proficient cells for topotecan and gemcitabine, respectively; loss of MMR had no effect on the rate of generation of variants resistant to paclitaxel. We conclude that the loss of MMR increases the ability of cisplatin to generate variants resistant to topotecan, gemcitabine, and possibly paclitaxel and that MMR also plays a role in controlling the spontaneous rate of generation of variants resistant to topotecan and gemcitabine.
MexXY multidrug efflux system of Pseudomonas aeruginosa

Anti-pseudomonas aminoglycosides, such as amikacin and tobramycin, are used in the treatment of Pseudomonas aeruginosa infections. However, their use is linked to the development of resistance. During the last decade, the MexXY multidrug efflux system has been comprehensively studied, and numerous reports of laboratory and clinical isolates have been published. This system has been increasingly recognized as one of the primary determinants of aminoglycoside resistance in P. aeruginosa. In P. aeruginosa cystic fibrosis isolates, upregulation of the pump is considered the most common mechanism of aminoglycoside resistance. Non-fermentative Gram-negative pathogens possessing very close MexXY orthologs such as Achromobacter xylosoxidans and various Burkholderia species (e.g., Burkholderia pseudomallei and B. cepacia complexes), but not B. gladioli, are intrinsically resistant to aminoglycosides. Here, we summarize the properties (e.g., discovery, mechanism, gene expression, clinical significance) of the P. aeruginosa MexXY pump and other aminoglycoside efflux pumps such as AcrD of Escherichia coli, AmrAB-OprA of B. pseudomallei, and AdeABC of Acinetobacter baumannii. MexXY inducibility of the PA5471 gene product, which is dependent on ribosome inhibition or oxidative stress, is noteworthy. Moreover, the discovery of the cognate outer membrane component (OprA) of MexXY in the multidrug-resistant clinical isolate PA7, serotype O12 deserves special attention.
EVOLUTIONARY AND HISTORICAL ANALYSIS OF PROTEIN VARIATION IN THE BLOTCHED FORMS OF SALAMANDERS OF THE ENSATINA COMPLEX (AMPHIBIA: PLETHODONTIDAE)

Geographic variation in 23 to 29 protein‐encoding genetic loci was examined in 48 populations of the Ensatina complex, a “ring species” distributed around the Central Valley of California. The samples span two critical links in the chain of morphologically distinct units: the transition from the unblotched to blotched color pattern types in the vicinity of Lassen Peak, northeastern California, and a geographic gap in the range of the complex in the San Gabriel Mountains, southern California. A general pattern of isolation by distance with a regular buildup of genetic distance correlated with increases in geographic distance characterizes the populations studied, with the exception of a little‐differentiated group of populations in the northern Sierra Nevada; this region is postulated to be a zone of genetic reticulation characterized by relatively high gene flow. An adaptively significant color pattern is thought to have spread into the northern Sierra Nevada from the south, but protein variants have been introduced both from the north and the south. Genetic distances across the San Gabriel Mountain gap match expectations from the pattern of buildup of genetic distance as a function of geographic distance elsewhere in the complex. A phylogenetic analysis of the protein data supports the reticulation hypothesis; whereas the southernmost populations currently do constitute a monophyletic assemblage, an “extinction experiment” demonstrates that the distinction could be the result of the recent extinction of populations in a present gap in our sampling. The Ensatina complex appears to be a dynamic entity representing several stages in the evolution of species. It is a ring species, and whereas various taxonomic arrangements are possible, no taxonomic changes are proposed.
Dissection of a Complex Disease Susceptibility Region Using a Bayesian Stochastic Search Approach to Fine Mapping

Identification of candidate causal variants in regions associated with risk of common diseases is complicated by linkage disequilibrium (LD) and multiple association signals. Nonetheless, accurate maps of these variants are needed, both to fully exploit detailed cell specific chromatin annotation data to highlight disease causal mechanisms and cells, and for design of the functional studies that will ultimately be required to confirm causal mechanisms. We adapted a Bayesian evolutionary stochastic search algorithm to the fine mapping problem, and demonstrated its improved performance over conventional stepwise and regularised regression through simulation studies. We then applied it to fine map the established multiple sclerosis (MS) and type 1 diabetes (T1D) associations in the IL-2RA (CD25) gene region. For T1D, both stepwise and stochastic search approaches identified four T1D association signals, with the major effect tagged by the single nucleotide polymorphism, rs12722496. In contrast, for MS, the stochastic search found two distinct competing models: a single candidate causal variant, tagged by rs2104286 and reported previously using stepwise analysis; and a more complex model with two association signals, one of which was tagged by the major T1D associated rs12722496 and the other by rs56382813. There is low to moderate LD between rs2104286 and both rs12722496 and rs56382813 (r2 ≃ 0.3) and our two SNP model could not be recovered through a forward stepwise search after conditioning on rs2104286. Both signals in the two variant model for MS affect CD25 expression on distinct subpopulations of CD4+ T cells, which are key cells in the autoimmune process. The results support a shared causal variant for T1D and MS. Our study illustrates the benefit of using a purposely designed model search strategy for fine mapping and the advantage of combining disease and protein expression data.
Development of a Friction Law Respecting Plastic Surface Smoothing

Friction has an essential influence on metal forming processes and affects the mould filling strongly. Numerical simulation is widely used because they allow for a efficient product design without the time and cost intensive production of prototype moulds. The quality of the simulation results and thus their reliability is determined by the accuracy of the modelling. For this purpose the applied friction law is of great importance. Characteristic of sheet-bulk metal forming is the coexistence of moderate contact pressures like in sheet metal forming and high contact pressures like in bulk metal forming. The Coulomb friction law is suitable for the sheet metal forming process but it predicts too high friction forces for high contact pressures. On the other hand the Tresca friction law is suitable for bulk metal forming but overestimates the friction for low contact pressures. A smooth transition between the Coulomb and Tresca friction law is described by the Shaw friction law and the Wanheim-Bay friction law. An unresolved problem remains the influence of plastic surface smoothing of structured workpiece surfaces. The tribological properties of the surface are altered by the plastic deformation of the surface roughness. As a consequence the real area of contact and thus the friction are larger in unloading and reloading than in the first loading at the same surface pressure. This plays a role in forming processes with multiple stages, where the surface is smoothed by prior forming operations like for example the forming of tailored blanks. Therefore efforts have been made in the numerical modelling of elasto-plastic surface deformation with a halfspace model. This model allows for the efficient modelling of large rough surfaces because it uses only a surface mesh and not an numerically expensive volume mesh like a Finite-Element model. This halfspace model is calibrated and verified with experimental investigations. A friction law taking into account the plastic surface deformation has been developed based on the halfspace simulations. It distinguishes between first loading, where the current surface pressure is higher than all surface pressures which occurred previously, and unloading or reloading, where the friction is higher because the surface is smoothed plastically in a previous load step, where the surface pressure was higher than currently.
Sensitivity and predictive value of criteria for p53germline mutation screening

Editor—The history of Li-Fraumeni syndrome (LFS) is a good illustration of the delineation of dominantly inherited family cancer syndromes. The identification of this syndrome is the result of the combination of two kinds of evidence, firstly, a number of reports on particular familial aggregations1 ,2 and, secondly, systematic family studies of childhood sarcomas.3-6 Among these studies, the decisive contribution came from Li and Fraumeni3 who were the first to publish the results of a family study on 641 children with rhabdomyosarcoma which led to the identification of four families in which a sib or a cousin was affected by rhabdomyosarcoma or another soft tissue sarcoma (STS). These families also had several members who were affected by diverse types of malignant tumours, in particular sarcomas and breast cancer at a very young age. This prompted the authors to propose the existence of a new familial syndrome.7 A prospective study on these families over 12 years provided evidence of a strong predisposition to cancer with a strikingly high frequency of multiple tumours.8 The term “Li-Fraumeni syndrome” was used for the first time in 19829 and the criteria, which subsequently became the classical definition of the syndrome, were proposed by Li and Fraumeni in 1988.10 These were a proband with a sarcoma before 45 years of age, a first degree relative with cancer before this age, and another close (first or second degree) relative in the lineage with either cancer before this age or a sarcoma at any age. These criteria led to the selection of 24 families which exhibited a wide variety of tumours including bone sarcomas, STS, breast cancer, brain tumours, leukaemia, adrenocortical carcinoma, lymphoma, lung, stomach, pancreas, and prostate cancer, but only the first six types were significantly in excess …
Clinical characteristics of unilateral myopic anisometropia in a juvenile optometric practice population

Purpose: A retrospective study of longitudinal case histories, undertaken to establish the clinical and statistical characteristics of unilateral myopic anisometropia (UMA) amongst the juvenile and adolescent population at an optometric practice, is reported. UMA was defined as that specific refractive state where an unequivocally myopic eye is paired with a ‘plano’ [spherical equivalent refraction, (SER) = ±0.25 Dioptres (D)] companion eye.
Role of Lipid Peroxidation Products, Plasma Total Antioxidant Status, and Cu-, Zn-Superoxide Dismutase Activity as Biomarkers of Oxidative Stress in Elderly Prediabetics

The relationship between hyperglycemia and oxidative stress in diabetes is well known, but the influence of metabolic disturbances recognized as prediabetes, in elderly patients especially, awaits for an explanation. Methods. 52 elderly persons (65 years old and older) with no acute or severe chronic disorders were assessed: waist circumference (WC), body mass index (BMI), percentage of body fat (FAT), and arterial blood pressure. During an oral glucose tolerance test (OGTT) fasting (0′) and 120-minute (120′) glycemia and insulinemia were determined, and type 2 diabetics (n = 6) were excluded. Subjects were tested for glycated hemoglobin HbA1c, plasma lipids, total antioxidant status (TAS), thiobarbituric acid-reacting substances (TBARS), and activity of erythrocyte superoxide dismutase (SOD-1). According to OGTT results, patients were classified as normoglycemics, (NGT, n = 18) and prediabetics, (PRE, n = 28). Results. Both groups did not differ with their lipids, FAT, and TBARS. PRE group had higher WC (P < 0.002) and BMI (P < 0.002). Lower SOD-1 activity (P < 0.04) and TAS status (P < 0.04) were found in PRE versus NGT group. Significance. In elderly prediabetics, SOD-1 and TAS seem to reflect the first symptoms of oxidative stress, while TBARS are later biomarkers of oxidative stress.
Convergence rates for the classical, thin and fractional elliptic obstacle problems

We review the finite-element approximation of the classical obstacle problem in energy and max-norms and derive error estimates for both the solution and the free boundary. On the basis of recent regularity results, we present an optimal error analysis for the thin obstacle problem. Finally, we discuss the localization of the obstacle problem for the fractional Laplacian and prove quasi-optimal convergence rates.
Decreased carboxylesterases expression and hydrolytic activity in type 2 diabetic mice through Akt/mTOR/HIF-1α/Stra13 pathway

Abstract 1. This study investigated the alteration of carboxylesterases in type 2 diabetes. We found that the carboxylesterase 1d (Ces1d) and carboxylesterase 1e (Ces1e) expression and the capacity of hydrolytic activity of liver and intestine decreased, whereas the Akt/mTOR/HIF-1α/ Stra13 (DEC1) signaling was activated in T2D mice. Consistently, high insulin could give rise to the same results in the high-glucose DMEM condition, which mimicked T2D, in primary mouse hepatocytes. 2. Perifosine or rapamycin almost abolished the decrease of the Ces1d and Ces1e expression and the hydrolytic activity induced by the insulin in the primary mouse hepatocytes. 3. The responsiveness of human hepatoma (HepG2) cells to high insulin in high-glucose condition was similar to that of primary mouse hepatocytes in terms of the altered expression of carboxylesterases. 4. The knockdown of HIF-1α or DEC1 with shRNA construct abrogated the decrease of the CES1 and CES2 expression induced by the insulin in high glucose condition in HepG2 cells. 5. Taken together, the decreased carboxylesterases expression and hydrolytic activity in T2D mice are through the Akt/mTOR/HIF-1α/Stra13 (DEC1) pathway.
Involved-nodal radiation therapy as a component of combination therapy for limited-stage Hodgkin's lymphoma: a question of field size.

PURPOSE Combined-modality therapy is the standard of care for limited-stage Hodgkin's lymphoma (HL). Radiation therapy has evolved from extended-field radiation therapy (EFRT) to involved-field radiation therapy (IFRT), reducing toxicity while maintaining high cure rates. Recent publications recommend a further reduction to involved-nodal radiation therapy (INRT), however, this has not been clinically validated. PATIENTS AND METHODS We identified 325 patients with limited-stage HL, diagnosed between May 1, 1989 and April 1, 2005, and treated with chemotherapy and radiation therapy following era-specific guidelines: EFRT until 1996; IFRT from 1996 to 2001; INRT < or = 5 cm from 2001 to the present. INRT < or = 5 cm was defined as the prechemotherapy nodal volume with margins < or = 5 cm to account for physiological movement, set-up variation, and the limitations of conventional simulation and radiation therapy techniques. Exclusion criteria were age younger than 16, fluorine-18 fluorodeoxyglucose positron emission tomography, non-doxorubicin, bleomycin, vinblastine, and dacarbazine-like chemotherapy, and/or more than four chemotherapy cycles. RESULTS At diagnosis, median age was 35 years; 52% male; stage IA 29%; stage IIA 71%. Ninety-five percent of patients received two chemotherapy cycles. The three radiation therapy groups were: EFRT, 39%; IFRT, 30%; and INRT < or = 5 cm, 31%. Median follow-up of living patients was 80 months. Median time to relapse was 37 months. Twelve relapses occurred: four after EFRT (3%); five after IFRT (5%); and three after INRT < or = 5 cm (3%; P = .9). No marginal recurrences occurred after INRT < or = 5 cm. Locoregional relapse (LRR) occurred in five patients: three after EFRT; two with IFRT; and none with INRT < or = 5 cm. At 5 years, progression-free survival (PFS) was 97%, and overall survival (OS) was 95%. At 10 years, PFS and OS were 95% and 90%, respectively. CONCLUSION Reduction in field size appears to be safe, without an increased risk of LRR in patients receiving INRT < or = 5 cm.
Origin of the glomerular basement membrane visualized after in vivo labeling of laminin in newborn rat kidneys

To examine the origin and assembly of glomerular basement membranes (GBMs), affinity purified anti-laminin IgG was directly coupled to horseradish peroxidase (HRP) and intravenously injected into newborn rats. Kidneys were then processed for peroxidase histochemistry and microscopy. Within 1 h after injection, anti-laminin bound to basement membranes of nephrons in all developmental stages (vesicle, comma, S- shaped, developing capillary loop, and maturing glomeruli). In S-shaped and capillary loop glomeruli, anti-laminin-HRP labeled a double basal lamina between the endothelium and epithelium. Sections incubated with anti-laminin in vitro showed labeling within the rough endoplasmic reticulum of endothelium and epithelium, indicating that both cell types synthesized laminin for the double basement membrane. In maturing glomeruli, injected anti-laminin-HRP bound throughout the GBMs, and double basement membranes were rarely observed. At this stage, however, numerous knobs or outpockets of basement membrane material extending far into the epithelial side of the capillary wall were identified and these were also labeled throughout their full thickness. No such outpockets were found in the endothelial cell layer of newborn rats (and they normally are completely absent in fully mature, adult glomeruli). In contrast with these results, in kidneys fixed 4-6 d after anti-laminin IgG-HRP injection, basement membranes of vesicle, comma, and S-shaped nephrons were unlabeled, indicating that they were assembled after injection. GBM labeling was seen in maturing glomeruli, however. In addition, the outpockets of basement membrane extending into the epithelium were often completely unlabeled whereas GBMs lying immediately beneath them were labeled intensely, which indicates that the outpockets were probably assembled by the epithelium. Injections of sheep anti-laminin IgG followed 8 d later with injections of biotin- rabbit anti-laminin IgG and double-label immunofluorescence microscopy confirmed that GBM formation continued during individual capillary loop expansion. GBM assembly therefore occurs by at least two different processes at separate times in development: (a) fusion of endothelial and epithelial basement membranes followed by (b) addition of new basement membrane from the epithelium into existing GBMs.
On Fast-Decodable Space–Time Block Codes

We focus on full-rate, fast-decodable space-time block codes (STBCs) for 2 times 2 and 4times2 multiple-input multiple-output (MIMO) transmission. We first derive conditions and design criteria for reduced-complexity maximum-likelihood (ML) decodable 2times2 STBCs, and we apply them to two families of codes that were recently discovered. Next, we derive a novel reduced-complexity 4times2 STBC, and show that it outperforms all previously known codes with certain constellations.
Risk Sensitive, Nonlinear Optimal Control: Iterative Linear Exponential-Quadratic Optimal Control with Gaussian Noise

In this contribution, we derive ILEG, an iterative algorithm to find risk sensitive solutions to nonlinear, stochastic optimal control problems. The algorithm is based on a linear quadratic approximation of an exponential risk sensitive nonlinear control problem. ILEG allows to find risk sensitive policies and thus generalizes previous algorithms to solve nonlinear optimal control based on iterative linear-quadratic methods. Depending on the setting of the parameter controlling the risk sensitivity, two different strategies on how to cope with the risk emerge. For positive-value parameters, the control policy uses high feedback gains whereas for negative-value parameters, it uses a robust feedforward control strategy (a robust plan) with low gains. These results are illustrated with a simple example. This note should be considered as a preliminary report.
Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity.