Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial Oxidative Stress Plays a Key Role in Aging and Apoptosis

Harman first suggested in 1972 that mitochondria might be the biological clock in aging, noting that the rate of oxygen consumption should determine the rate of accumulation of mitochondrial damage produced by free radical reactions. Later in 1980 Miquel and coworkers proposed the mitochondrial theory of cell aging. Mitochondria from postmitotic cells use O2 at a high rate, hence releasing oxygen radicals that exceed the cellular antioxidant defences. The key role of mitochondria in cell aging has been outlined by the degeneration induced in cells microinjected with mitochondria isolated from fibroblasts of old rats, especially by the inverse relationship reported between the rate of mitochondrial production of hydroperoxide and the maximum life span of species. An important change in mitochondrial lipid composition is the age‐related decrease found in cardiolipin content. The concurrent enhancement of lipid peroxidation and oxidative modification of proteins in mitochondria further increases mutations and oxidative damage to mitochondrial DNA (mtDNA) in the aging process. The respiratory enzymes containing the defective mtDNA‐encoded protein subunits may increase the production of reactive oxygen species, which in turn would aggravate the oxidative damage to mitochondria. Moreover, superoxide radicals produced during mitochondrial respiration react with nitric oxide inside mitochondria to yield damaging peroxynitrite. Treatment with certain antioxidants, such as sulphur‐containing antioxidants, vitamins C and E, or the Ginkgo biloba extract EGb 761, protects against the ageassociated oxidative damage to mtDNA and the oxidation of mitochondrial glutathione. Moreover, the EGb 761 extract also prevents changes in mitochondrial morphology and function associated with aging of the brain and liver.
The Genetics Home Reference: A New NLM Consumer Health Resource

The Genetics Home Reference (GHR) is a new information resource developed to be part of the National Library of Medicine's (NLM's) consumer health initiatives. The GHR's guiding principle is to make the health implications of the Human Genome Project accessible to the public. The GHR accomplishes this by providing a bridge between the NLM's consumer health systems MEDLINEplus and ClinicalTrials.gov on the one hand and the multiple resources emanating from the Human Genome Project on the other. The initial focus is on single gene conditions that are main topics in MEDLINEplus.
Molecular characterization of plasmids pS7a and pS7b from Lactococcus lactis subsp. lactis bv. diacetylactis S50 as a base for the construction of mobilizable cloning vectors

Aims: Strain Lactococcus lactis subsp. lactis bv. diacetylactis S50 harbours five theta‐replicating plasmids (pS6, pS7a, pS7b, pS80 and pS140). The aim of this study was to characterize domains involved in the replication and conjugative mobilization of the small plasmids pS7a and pS7b, which are structurally very similar.
Permanent magnets models and losses in 2D FEM simulation of electrical machines

This paper presents different methods to model permanent magnet materials within the 2D finite element simulation of electrical machines and discuss them. The modeling deals with both the material magnetic properties and the circuit equations related to different parts of the machine. The emphasis is on modeling permanent magnets as part of the rotor electrical circuit. The methods presented are compared through the simulations of a previously designed machine. The simulations show large differences in the computed PM and other operation quantities of the machine due to the coupling between the filed and circuit equations. The choice of the rotor material is also discussed from the view point of losses. Low-loss lamination is found to be a better choice than solid-steel rotor construction used in some machines. Further, the inclusion of the Joule and permanent magnet losses in the field solution leads to more accurate estimation of the currents and torque.
Plasma protein map: An update by microsequencing

The reference plasma protein map, obtained with immobilized pH gradients in the first dimension of two‐dimensional electrophoresis, is presented. By microsequencing, more than 40 polypeptide chains were identified. The new polypeptides and previously known proteins are listed in a table and labeled on the protein map, thus providing an update of the human plasma two‐dimensional gel database.
Alternative measures of electronic health record adoption among hospitals.

OBJECTIVE To develop measures of the use of electronic health records (EHRs) that accurately reflect the full continuum of hospital adoption and progress toward meaningful use and to understand the intercorrelations and patterns associated with hospital adoption of specific EHR functions. STUDY DESIGN This study analyzed the 2009 American Hospital Association (AHA) information technology (IT) supplement survey. The main section of this survey assessed the adoption and use of 24 EHR functionalities in the following major categories: electronic clinical documentation, results viewing, computerized provider order entry, and clinical decision support. METHODS This study relied on descriptive statistical methods and a principal component factor analysis. RESULTS We found that 11.4% of hospitals met all and 48.3% met half or more of the core criteria that are included in both the AHA IT survey and the final "meaningful-use" rule. The results from our factor analysis imply that hospitals adopt groups of similar EHR functions, but choices to adopt across major categories are relatively independent. CONCLUSIONS Many hospitals have adopted multiple features of EHRs and tend to use a staged adoption strategy based on logical groupings of functions. These results indicate to policymakers that there is no single path toward adoption of advanced EHR systems.
Genetic differentiation among populations of Brachytrupes portentosus (Lichtenstein 1796) (Orthoptera: Gryllidae) in Thailand and the Lao PDR: the Mekong River as a biogeographic barrier

Abstract The Mekong River is known to act as a boundary between a number of terrestrial and freshwater species, including various parasites and their intermediate hosts as well as endangered mammal species. Little information is available, however, on the genetic differentiation between terrestrial invertebrates to the east and the west of this wide river. The genetic diversity among eight natural populations of Brachytrupes portentosus (Lichtenstein, 1796) (Orthoptera: Gryllidae) collected from Thailand and the Lao People's Democratic Republic (PDR) were analyzed by multilocus enzyme electrophoresis. The allelic profiles of 20 enzymes encoding 23 loci were analyzed. An average of 41% fixed differences was detected between the populations from Thailand and Lao PDR, which are separated by the Mekong River. The percent fixed differences ranged between 4% and 26% within the populations from Thailand and between 4% and 22% within the populations from Lao PDR. A phenogram shows that the eight populations fell into two major clusters based on the Thai and Lao sampling sites. The genetic distance between the samples within Thailand and within Lao PDR was related to the distances between sampling areas. The genetic variability between populations of this cricket indicates that genetic relationships are influenced by a natural barrier as well as by the geographical distance between these allopatric populations.
HIV‐1 RT‐associated ribonuclease H displays both endonuclease and 3′‐‐‐‐5′ exonuclease activity.

We have analysed the mechanism of ribonuclease H (RNaseH) induced cleavage of a defined RNA‐DNA hybrid by human immuno‐deficiency virus (HIV‐1) reverse transcriptase (RT). An in vitro transcribed RNA labelled at the 3′ end was hybridized to a pentadecameric DNA oligonucleotide complementary to an internal region of the RNA. Upon incubation of this RNA‐DNA hybrid with recombinant p66 or p66/p51 HIV‐1 reverse transcriptase, RT‐RNaseH mediated cleavage is observed at most nucleotides within the short hybridized stretch, resulting in a spectrum of RNA fragments extending from the 3′ label to this region and differing in length by one nucleotide. The same RNA, this time labelled at the 5′ end, yields only one or two major cleavage products corresponding to RNA species extending from the 5′ label to the middle of the hybridized region. Such a result can be explained by the action of both endonuclease and 3′‐‐‐‐5′ exonuclease activities inherent to the C‐terminal domain of p66 RT. To investigate how RNaseH cleavage is coupled to reverse transcription, a combination of deoxynucleoside triphosphates was used which allowed controlled extension of the primer DNA. Concomitantly with the elongation of the oligonucleotide primer, RNaseH cleavage proceeds towards the 5′ end of the RNA with identical increments, suggesting a simultaneous action of both activities.
Functional Characterization of the Multidomain F Plasmid TraI Relaxase-Helicase*

TraI, a bifunctional enzyme containing relaxase and helicase activities, initiates and drives the conjugative transfer of the Escherichia coli F plasmid. Here, we examined the structure and function of the TraI helicase. We show that TraI binds to single-stranded DNA (ssDNA) with a site size of ∼25 nucleotides, which is significantly longer than the site size of other known superfamily I helicases. Low cooperativity was observed with the binding of TraI to ssDNA, and a double-stranded DNA-binding site was identified within the N-terminal region of TraI 1–858, outside the core helicase motifs of TraI. We have revealed that the affinity of TraI for DNA is negatively correlated with the ionic strength of the solution. The binding of AMPPNP or ADP results in a 3-fold increase in the affinity of TraI for ssDNA. Moreover, TraI prefers to bind ssDNA oligomers containing a single type of base. Finally, we elucidated the solution structure of TraI using small angle x-ray scattering. TraI exhibits an ellipsoidal shape in solution with four domains aligning along one axis. Taken together, these data result in the assembly of a model for the multidomain helicase activity of TraI.
Scoliosis Correction Maintenance in Skeletally Immature Patients With Idiopathic Scoliosis: Is Anterior Fusion Really Necessary?

Study Design. A retrospective evaluation of the occurrence of the crankshaft phenomenon in skeletally immature patients with idiopathic scoliosis. Objective. To determine what factors, if any, contribute to a decreased occurrence of crankshaft phenomenon in patients treated with posterior surgery only. Summary of Background Data. Reports have described the progression of scoliotic deformity, termed the crankshaft phenomenon, in a region of solid posterior arthrodesis in skeletally immature patients. This has led some authors to advocate the use of concomitant anterior discectomy and fusion to prevent crankshaft. Methods. From 1989 through 1994, 18 Risser 0 patients with thoracic or thoracolumbar idiopathic scoliosis underwent Isola (De Puy-Acromed, Raynham, MA) posterior instrumentation and fusion. They were assessed for evidence of the crankshaft phenomenon, identified by coronal plane deformity progression of 10° or more, or a rib vertebra angle difference of 10° or more. The average age of the patients was 12.5 years (range, 10.5–15.5 years), and the average follow-up period was 39 months (range, 24–68 months). Results. Eleven patients (10 girls and 1 boy) had closed triradiate cartilage at the time of surgery. Their average Cobb angle was 62° before surgery, 21° after surgery, and 22° at follow-up assessment. No patients in this group met the criteria for crankshaft. Seven patients (6 girls and 1 boy) had open triradiate cartilage at the time of surgery. Their average Cobb angle was 62° before surgery, 18° after surgery, and 20° at follow-up evaluation. No patient had a 10° or more increase in rib vertebra angle difference. One patient had more than a 10° increase in her Cobb angle (11°) from postoperative to latest follow-up assessment. Her instrumentation construct, performed in 1989, used sublaminar wires as the caudal anchors. Hooks and pedicle screws are now used. Two of the seven patients with open triradiate cartilage underwent surgery during or before their peak height velocity and displayed no evidence of crankshaft. No deaths, neurologic complications, or infections occurred in either group. Conclusions. These findings suggest that scoliotic deformity progression can be prevented in skeletally immature patients with idiopathic scoliosis as young as 10 years of age with the use of stiff segmental posterior instrumentation, without the necessity of concomitant anterior arthrodesis.
Activity classification for real-time wearable systems: Effect of window length, sampling frequency and number of features on classifier performance

The aim of this study was to evaluate how the physical activity classification window length, accelerometer sampling frequency and the number of correlating features affect the classifier performance. It is important to study the effect of these elements in order to reduce the computational power and memory buffers needed for wearable systems, where classification is done in real-time. Three different window lengths (5 s, 3 s, 1s), sampling frequencies (50 Hz, 25 Hz, 13 Hz) and two feature sets (110 and 43 features) were tested and evaluated in this study. As a result, it was found that the classifier performed similarly with the window lengths of 5 s and 3 s and the sampling rates of 50 Hz and 25 Hz, but the results with the window length of 1 s or the sampling rate of 13 Hz were lower. No noticeable difference in classifier sensitivity was found by decreasing the number of features based on correlation.
Lower-limb exoskeletons for individuals with chronic spinal cord injury: findings from a feasibility study

Objective: To assess the feasibility of conducting a well-powered trial evaluating the neurological and functional effects of using an exoskeleton in individuals with chronic spinal cord injury. Design: A longitudinal, prospective, self-controlled feasibility study. Setting: Specialist Spinal Cord Injuries Centre, UK; 8 months during 2013–2014. Subjects: Individuals with chronic motor complete or incomplete spinal cord injury. Interventions: Enrolled subjects were assigned to 20 exoskeleton (ReWalk™, Argo Medical Technologies Ltd, Yokneam Ilit, Israel) training sessions over a 10-week training period. Main measures: Feasibility measures, clinical and mobility outcome measures and measures appraising subjects’ disability and attitude towards assistive technology were assessed before, during and after the study. Descriptive statistics were applied. Results: Out of 60 candidates, ten (17%) were enrolled and five (8%) completed the training programme. Primary reasons for not enrolling were ineligibility (n = 24, 40%) and limited interest to engage in a 10-week training programme (n = 16, 27%). Five out of ten enrolled subjects experienced grade I/II skin aberrations. While walking speeds were higher and walking distances were longer in all exoskeleton users when compared with non-use, the exoskeleton did generally not meet subjects’ high expectations in terms of perceived benefits. Conclusions: The conduct of a controlled trial evaluating the benefits of using exoskeletons that require a lengthy user-commitment to training of individuals with chronic motor complete or incomplete spinal cord injury comes with considerable feasibility challenges. Vigilance is required for preventing and detecting medical complications in spinal cord injury exoskeleton users.
De‐Novo Cholangiocarcinoma in the Setting of Recurrent Primary Sclerosing Cholangitis Following Liver Transplant

Orthotopic liver transplantation is the only definitive therapeutic option in patients with primary sclerosing cholangitis (PSC) and end‐stage liver disease. However, PSC recurs in up to 20% of patients transplanted for this indication. To date, no patient has been reported to develop cholangiocarcinoma (CCA) post‐transplant, without biliary tract cancer having been present pretransplant. Here, we report recurrent PSC complicated by de‐novo CCA in a 31‐year‐old man transplanted for PSC 8 years earlier. Cholangiocarcinoma was confirmed using a combination of computed tomography, cholangiography, positron emission tomography and histological examination of biliary cytology. He has since been successfully re‐transplanted following preoperative chemo‐radiotherapy. No viable tumor was identified in the explanted liver. This case establishes that long‐term complications associated with PSC and biliary‐enteric surgery such as CCA may become apparent in new grafts post‐transplant.
A hyper-heuristic clustering algorithm

The so-called heuristics have been widely used in solving combinatorial optimization problems because they provide a simple but effective way to find an approximate solution. These technologies are very useful for users who do not need the exact solution but who care very much about the response time. For every existing heuristic algorithm has its pros and cons, a hyper-heuristic clustering algorithm based on the diversity detection and improvement detection operators to determine when to switch from one heuristic algorithm to another is presented to improve the clustering result in this paper. Several well-known datasets are employed to evaluate the performance of the proposed algorithm. Simulation results show that the proposed algorithm can provide a better clustering result than the state-of-the-art heuristic algorithms compared in this paper, namely, k-means, simulated annealing, tabu search, and genetic k-means algorithm.
The language of Stratified Sets is confluent and strongly normalising

We study the properties of the language of Stratified Sets (first-order logic with $\in$ and a stratification condition) as used in TST, TZT, and (with stratifiability instead of stratification) in Quine's NF. We find that the syntax forms a nominal algebra for substitution and that stratification and stratifiability imply confluence and strong normalisation under rewrites corresponding naturally to $\beta$-conversion.
Non-uniform illumination correction in infrared images based on a modified fuzzy c-means algorithm

The correction of non-uniform illumination and the elimination of shading artifacts is an important preprocessing task used in a great number of image processing applications such as segmentation, registration or quantitative analysis. Although, a careful and accurate set up of the image acquisition system may degrade the importance of a brightness normalization algorithm, non-uniform illumination appears due to the interaction of objects and light on the scene requires retrospective shading correction. The image formation process and the corresponding shading effects are described by a linear image formation model, which consists of a multiplicative and an additive shading component. In this paper a novel brightness normalization method is proposed to eliminate the non-uniform illumination effects. The method is based on the application of a fuzzy c-means algorithm (FCM) only on the background part of the acquired image, where the objective function is modified to take into account local information of each pixel in the estimation of the multiplicative and the additive shading components. The modified FCM algorithm is iterative, as the standard FCM, and at each iteration the multiplicative and the additive shading components are re-estimated based on the cluster centers and the membership of each pixel in a specific cluster. Brightness correction is performed by the inverse of the image formation model after FCM convergence. Experiments were conducted in a database of both real and artificial infrared images. The experimental results show that the proposed method decreases significantly the non-uniform illumination effects and does not introduce brightness variations if the background is uniform.
The Organization of Electronic Markets: Contributions from the New Institutional Economics

Electronic markets are increasingly gaining scientific and economic attention. In order to realize their often postulated rationalization potential, a closer look into their organization is necessary. New institutional economics provides a body of theory well suited for this task. Transaction cost theory helps to understand why transactions are more often conducted via markets and why those markets require organization. Principal-agent theory explains future (dis-)intermediation structures in electronic markets. Finally, property rights theory helps to understand why a certain level of market intransparency will remain in electronic markets.
Chapter 9 Sedimentary development of the Mid-Permian–Mid-Triassic Maitai continental margin forearc basin, South Island, New Zealand

Abstract The Mid-Late Permian–Mid-Triassic Maitai Group is interpreted as the distal forearc basin of the SE Gondwana active continental margin. The basin initially received very coarse detritus (Upukerora Formation) from the recently emplaced, nearby Dun Mountain ophiolite and related oceanic-arc rocks. Early tectonic subsidence accommodated up to 1000 m of bioclastic gravity-flow deposits from an adjacent carbonate platform, together with terrigenous and volcanic arc-derived material (Wooded Peak Formation). Basin-levelling turbidites then accumulated, composed of mixed terrigenous and arc-derived igneous material, with bottom-current reworking (Tramway Formation). Latest Permian–earliest Triassic gravity-flow deposits (locally absent) are characterized by relatively basic volcanic material (Little Ben Formation). Overlying turbidites accumulated in a relatively oxygen-poor, deeper-water setting (Greville Formation). Fine-grained background sedimentation then switched to well-oxidized, with traction-current reworking (Waiua Formation). The overlying Early–Mid Triassic Stephens Subgroup included the accumulation of lenticular sandstone turbidites, channelized conglomerate, well-oxidized deep-sea mud and felsic tuff. Permian and Early Triassic marginal carbonate platforms collapsed and were emplaced as localized exotic blocks. Extrusive and intrusive clasts within channelized conglomerates (Snowdon Formation) were derived from the adjacent continental margin arc. The forearc basin was subsequently displaced to its present position, possibly with up to 3000 km of southwards translation.
Multiplex PCR assay to aid in the identification of the highly transmissible Mycobacterium tuberculosis strain CDC1551.

SETTING Mycobacterium tuberculosis strain CDC1551 outbreak area in Tennessee and Kentucky and selected locations in the USA. OBJECTIVE Develop a PCR assay to distinguish the highly transmissible CDC1551 from strains which have similar 4-band IS6110 fingerprints. DESIGN Compare the IS6110 insertion sites in CDC1551 with those in 10 isolates which have similar 4-band IS6110 fingerprints. Utilize unique characteristics of insertion sites in CDC1551 to design a multiplex PCR to identify this strain. RESULTS A multiplex PCR was developed which targets an IS6110 insertion conserved in most IS6110 low copy number strains and a deletion within the direct repeat region adjacent to an IS6110 insertion. Of 139 isolates with similar 4-band fingerprints, the CDC1551 PCR pattern was generated by only the 14 outbreak associated isolates. Of 154 isolates with different fingerprints, only four generated the CDC1551 pattern and these could be distinguished from CDC1551 by their IS6110 fingerprint. CONCLUSIONS The multiplex PCR used in conjunction with the IS6110 fingerprint should be a useful tool to aid in the continued surveillance of the outbreak area and follow the spread of this highly transmissible strain of M. tuberculosis.