Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Repair in the Context of Chromatin

Modulation of chromatin is essential to nuclear processes that utilize DNA, such as transcription, replication, and repair. For example, transcription is assisted by histone post-translational modifications, as well as chromatin-remodeling complexes, which alter the structure of chromatin. Furthermore, recent advancements in the fields of DNA repair and chromatin reveal that both histone modifications and chromatin-remodeling complexes are essential for the repair of DNA lesions. In particular, chromatin-modifying complexes, such as the INO80 chromatin-remodeling complex and the Tip60 histone acetyltransferase complex, associate with the DNA damage-induced phosphorylated H2AX, which is often referred to as ? -H2AX. In S. cerevisiae, the association of INO80 with ? -H2AX is required for the recruitment of INO80 to sites of DNA double-strand breaks. Additionally, in Drosophila, Tip60 exchanges ? -H2AX for unmodified H2A in regions of DNA damage. This report reviews recent studies that emphasize the intimate relationship between evolutionarily-conserved chromatin-modifying complexes and histone post-translational modifications in the repair of DNA damage.
Graphene: powder, flakes, ribbons, and sheets.

Graphene's unique physical and electrical properties (high tensile strength, Young's modulus, electron mobility, and thermal conductivity) have led to its nickname of "super carbon. " Graphene research involves the study of several different physical forms of the material: powders, flakes, ribbons, and sheets and others not yet named or imagined. Within those forms, graphene can include a single layer, two layers, or ≤10 sheets of sp² carbon atoms. The chemistry and applications available with graphene depend on both the physical form of the graphene and the number of layers in the material. Therefore the available permutations of graphene are numerous, and we will discuss a subset of this work, covering some of our research on the synthesis and use of many of the different physical and layered forms of graphene. Initially, we worked with commercially available graphite, with which we extended diazonium chemistry developed to functionalize single-walled carbon nanotubes to produce graphitic materials. These structures were soluble in common organic solvents and were better dispersed in composites. We developed an improved synthesis of graphene oxide (GO) and explored how the workup protocol for the synthesis of GO can change the electronic structure and chemical functionality of the GO product. We also developed a method to remove graphene layers one-by-one from flakes. These powders and sheets of GO can serve as fluid loss prevention additives in drilling fluids for the oil industry. Graphene nanoribbons (GNRs) combine small width with long length, producing valuable electronic and physical properties. We developed two complementary syntheses of GNRs from multiwalled carbon nanotubes: one simple oxidative method that produces GNRs with some defects and one reductive method that produces GNRs that are less defective and more electrically conductive. These GNRs can be used in low-loss, high permittivity composites, as conductive reinforcement coatings on Kevlar fibers and in the fabrication of large area transparent electrodes. Using solid carbon sources such as polymers, food, insects, and waste, we can grow monolayer and bilayer graphene directly on metal catalysts, and carbon-sources containing nitrogen can produce nitrogen-doped graphene. The resulting graphene can be transferred to other surfaces, such as metal grids, for potential use in transparent touch screens for applications in personal electronics and large area photovoltaic devices. Because the transfer of graphene from one surface to another can lead to defects, low yields, and higher costs, we have developed methods for growing graphene directly on the substrates of interest. We can also produce patterned graphene to make GNRs or graphane/graphene superlattices within a single sheet. These superlattices could have multiple functions for use in sensors and other devices. This Account only touches upon this burgeoning area of materials chemistry, and the field will continue to expand as researchers imagine new forms and applications of graphene.
The Clinicopathologic Significance of the Loss of BAF250a (ARID1A) Expression in Endometrial Carcinoma

Objective AT-rich interactive domain 1A (ARID1A) is a tumor suppressor gene that encodes the BAF250a protein. Recent studies have shown the loss of ARID1A expression in several types of tumors. We aimed to investigate the clinical and pathologic role of BAF250a in endometrial carcinoma. Methods We examined the expression of BAF250a and its correlation with the expression of p53, estrogen receptor, progesterone receptor, glucocorticoid receptor, hypoxiainduciblefactor-1&agr;, and vascular endothelial growth factor in normal and various malignant endometrial tissues. Results The expression of BAF250 was significantly down-regulated in endometrial carcinoma when compared with normal endometrial tissues. The loss of BAF250a expression was found in 25% of endometrial carcinoma samples but not in normal endometrial tissues, complex endometrial hyperplasia, and atypical endometrial hyperplasia samples. Subtypes of endometrial carcinoma, especially uterine endometrioid carcinoma and uterine clear cell carcinoma, had higher frequency of loss of BAF250a expression. In addition, the expression of BAF250a was positively correlated with estrogen receptor and negatively correlated with p53 in poorly differentiated endometrial adenocarcinoma. Moreover, the expression of BAF250a was significantly associated with the differentiation status of endometrial carcinoma but not associated with clinical stage, the depth of myometrial invasion, lymph node metastasis, and overall survival of patients with endometrial carcinoma. Conclusions Our data showed that loss of BAF250a is frequently found in high-grade endometrioid and clear cell carcinomas but not in other types of endometrial carcinoma. The loss of BAF250a expression does not have prognostic value for endometrial carcinoma.
Free energy distributions in proteins

Protein molecules in solution have a broad distribution of enthalpy states. A good approximation to the distribution function for enthalpy states can be calculated, using the maximum‐entropy method, from the moments of the distribution that, in turn, are obtained from the experimental temperature dependence of the heat capacity. In the present paper, we show that the enthalpy probability distribution can then be formulated in terms of a free energy function that gives the free energy of the protein corresponding to a particular value of the enthalpy. By the location of the minima in this function, the free energy distribution graphically indicates the most probable values of the enthalpy for the protein. We find that the behavior of the free energy functions for proteins falls somewhere between two different cases: a two‐state like function with two minima, the relative levels of the two states changing with temperature; and, a single‐minimum function where the position of the minimum shifts to higher enthalpy values as the temperature is increased. We show that the temperature dependence of the free energy function can be expressed in terms of a central free energy distribution for a given, fixed temperature (which is most conveniently chosen as the temperature of the maximum in the heat capacity). The nature of this central free energy function for a given protein thus yields all of the thermodynamic behavior of that protein over the temperature range of the denaturation process. Proteins 2001;45:325–336. © 2001 Wiley‐Liss, Inc.
Application-Oriented Comparison and Evaluation of Six Semantic Similarity Measures Based on Wordnet

In the task of auto-building a Chinese-English semantic lexicon for translation selection, this research presents a method, which introduces WordNet similarity measures to wash out misaligned Chinese-English word pairs. Six different proposed measures of similarity based on WordNet were experimentally compared and evaluated by using WordNet and the software package WordNet::Similarity. It was found that the leader measure is res and lch, then wup, lin takes the fourth place, then jcn, and random is the tailender
Cloning and Characterization of the Zymobacter palmae Pyruvate Decarboxylase Gene (pdc) and Comparison to Bacterial Homologues

ABSTRACT Pyruvate decarboxylase (PDC) is the key enzyme in all homo-ethanol fermentations. Although widely distributed among plants, yeasts, and fungi, PDC is absent in animals and rare in bacteria (established for only three organisms). Genes encoding the three known bacterial pdc genes have been previously described and expressed as active recombinant proteins. The pdc gene from Zymomonas mobilis has been used to engineer ethanol-producing biocatalysts for use in industry. In this paper, we describe a new bacterial pdc gene from Zymobacter palmae. The pattern of codon usage for this gene appears quite similar to that for Escherichia coli genes. In E. coli recombinants, the Z. palmae PDC represented approximately 1/3 of the soluble protein. Biochemical and kinetic properties of the Z. palmae enzyme were compared to purified PDCs from three other bacteria. Of the four bacterial PDCs, the Z. palmae enzyme exhibited the highest specific activity (130 U mg of protein−1) and the lowest Km for pyruvate (0.24 mM). Differences in biochemical properties, thermal stability, and codon usage may offer unique advantages for the development of new biocatalysts for fuel ethanol production.
Separation of outer and cytoplasmic membranes of Fibrobacter succinogenes and membrane and glycogen granule locations of glycanases and cellobiase

The outer membrane (OM) of Fibrobacter succinogenes was isolated by a combination of salt, sucrose, and water washes from whole cells grown on either glucose or cellulose. The cytoplasmic membrane (CM) was isolated from OM-depleted cells after disruption with a French press. The OM and membrane vesicles isolated from the extracellular culture fluid of cellulose-grown cells had a higher density, much lower succinate dehydrogenase activity, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein profiles different from those of the CM. The OM from both glucose- and cellulose-grown cells and the extracellular membrane vesicles from cellulose-grown cultures exhibited higher endoglucanase, xylanase, and acetylesterase activities than the CM and other cell fractions. Endoglucanase 2 was absent from the isolated OM fractions of glucose- and cellulose-grown cells and from the extracellular membrane vesicles of cellulose-grown cells but was present in the CM and intracellular glycogen granule fractions, while endoglucanase 3 was enriched in the OM. Cellobiosidase was located primarily in the periplasm as previously reported, while cellobiase was mainly present in the glycogen granule fraction of glucose-grown cells and in a nongranular glycogen and CM complex in cellulose-grown cells. The cellobiase was not eluted from glycogen granules by cellobiose, maltose, and maltotriose nor from either the granules or the cell membranes by nondenaturing detergents but was eluted from both glycogen granules and cell membranes by high concentrations of salts. The eluted cellobiase rebound almost quantitatively when diluted and mixed with purified glycogen granules but exhibited a low affinity for Avicel cellulose. Thus, we have documented a method for isolation of OM from F. succinogenes, identified the OM origin of the extracellular membrane vesicles, and located glycanases and cellobiase in membrane and glycogen fractions.
Transsplenic percutaneous nephrolithotomy.

BACKGROUND AND PURPOSE Percutaneous nephrolithotomy (PNL) is the treatment of choice for patients with large or complex renal calculi. Although injuries to intra-abdominal organs are rare during PNL, splenic injuries have been reported. The management of a splenic injury after PNL is not well defined; therefore, we performed a study to define a management strategy for such an event. PATIENTS AND METHODS A retrospective, multi-institutional study was performed to identify all cases of splenic injury that occurred during PNL. All procedures were performed as a single-stage operation, with percutaneous access obtained in the operating room by the urologist. A review of patient records and imaging was conducted to identify treatment strategies and outcomes. RESULTS Three patients were identified as having undergone a transsplenic PNL. All puncture sites were upper pole, supracostal access of the left kidney. All cases of injury were identified after the procedure, with two stable patients' injuries identified on postoperative CT scan, and a third patient presenting with significant bleeding at removal of the nephrostomy tube. The spleen-preserving, conservative management strategy was successful, because no patients needed exploratory surgery. CONCLUSION Splenic injury is a rare complication sustained most commonly during supracostal, upper-pole access to the left renal unit. When patients are hemodynamically stable, this complication can be conservatively managed, with prolonged nephrostomy drainage and observation in a monitored setting before and after nephrostomy tube removal.
Monte Carlo simulation of a disclination core in nematic solutions of rodlike molecules.

The core structure of a disclination line defect in a nematic liquid crystal is simulated by a Monte Carlo technique in which molecules are represented as hard spherocylinders, with aspect ratios ranging from 5 to 15. For small aspect ratios (5 and 8), we confirm the mean-field Landau theory that the core is biaxial with negative order parameter at the center. The order parameter coherence length is small, of the order of the molecular diameter. For large aspect ratios, we discover a new microscopically ``escaped'' structure for -1/2 wedge disclinations, in which the molecules point predominantly along the disclination line. Free energy calculations demonstrate that the ``escaped'' structure is of lower energy than the unescaped ``flat'' structure, which is metastable. We expect the ``escaped'' structure to retard disclination mobility.
Is Psychopathology Part of the Phenotypic Spectrum of Myoclonus-dystonia?: A Study of a Large Dutch M-D Family

BackgroundMyoclonus-dystonia (M-D) is a movement disorder frequently caused by mutations in the epsilon-sarcoglycan gene (SGCE, DYT11). In several M-D families, psychiatric symptoms accompanying the motor symptoms have been reported, but a shared genetic etiology remains unclear. ObjectiveTo assess neuropsychologic functioning and psychopathology in DYT11 mutation carriers (MC) and their family members using standardized neuropsychologic and psychiatric measures. MethodsCognitive and behavioural characteristics of 27 DYT11 MC (14 symptomatic and 13 asymptomatic) and 42 control subjects from 1 large Dutch M-D family were studied. Neuropsychologic tests encompassed memory, language, mental speed, concentration, visuospatial function, and executive functions. Psychiatric assessment addressed qualitative (according to Diagnostic and Statistical Manual-IV criteria) as well as quantitative measures of depression, anxiety, panic attacks, and obsessive-compulsive disorder (OCD), using selfadministered and interview-based scales. ResultsNo differences were observed on tests of cognitive functioning between DYT11 MC and controls. The frequency of Diagnostic and Statistical Manual-IV diagnoses was higher in the symptomatic DYT11 MC than in controls. The symptomatic DYT11 MC showed more depressive and anxiety symptoms, including panic attacks but no increase of OCD compared with controls. No differences were found between asymptomatic DYT11 MC and controls on any of the psychopathologic tests. ConclusionsNeither cognitive dysfunction nor OCD seems to be associated with the DYT11 phenotype in this large Dutch pedigree. Depressive and anxiety symptoms are increased in symptomatic, but not in asymptomatic DYT11 MC. Future research has to be carried out to determine whether the psychiatric symptoms are part of or secondary to the DYT11 phenotype.
Machine Learning Algorithms : A Review

– In this paper, various machine learning algorithms have been discussed. These algorithms are used for various purposes like data mining, image processing, predictive analytics, etc. to name a few. The main advantage of using machine learning is that, once an algorithm learns what to do with data, it can do its work automatically.
MTMR: A conceptual interior design framework integrating Mixed Reality with the Multi-Touch tabletop interface

This paper introduces a conceptual interior design framework - Multi-Touch Mixed Reality (MTMR), which integrates mixed reality with the multi-touch tabletop interface, to provide an intuitive and efficient interface for collaborative design and an augmented 3D view to users at the same time. Under this framework, multiple designers can carry out design work simultaneously on the top view displayed on the tabletop, while live video of the ongoing design work is captured and augmented by overlaying virtual 3D furniture models to their 2D virtual counterparts, and shown on a vertical screen in front of the tabletop. Meanwhile, the remote client's camera view of the physical room is augmented with the interior design layout in real time, that is, as the designers place, move, and modify the virtual furniture models on the tabletop, the client sees the corresponding life-size 3D virtual furniture models residing, moving, and changing in the physical room through the camera view on his/her screen. By adopting MTMR, which we argue may also apply to other kinds of collaborative work, the designers can expect a good working experience in terms of naturalness and intuitiveness, while the client can be involved in the design process and view the design result without moving around heavy furniture. By presenting MTMR, we hope to provide reliable and precise freehand interactions to mixed reality systems, with multi-touch inputs on tabletop interfaces.
Renal carcinoid tumour.

A 43 year old female presented to her local physician with a vague history of left flank pain, abdominal discomfort and haematuria. She was investigated and ultrasonography demonstrated a large mass in the left kidney. Left nephrectomy was performed. The specimen consisted of a kidney measuring 12.5 x 7.8 x 5.8cms. On sectioning, part of the kidney was replaced at the lower pole by a tan coloured circumscribed mass measuring 7.5 x 6.5 x 5.3 cms. Foci of necrosis and haemorrhage were also seen (Figure 1). Histopathological examination showed a neoplasm composed of tubules and acini lined by cells with uniform round nuclei and pink cytoplasm (Figure 2). Occasional mitoses were seen. The sections were stained with a panel of monoclonal antibodies using the PAP technique. The tumour cells showed positivity for Chromogranin, Neuron Specific Enolase, Synaptophysin, Vimentin, Cytokeratins MNF and CAM 5.2. Sections from hilar blood vessels and ureteric margin of excision revealed no evidence of tumour. There was no pathological evidence of extra renal spread of the tumour. Invasion of the perirenal fat was not seen. Eight months after surgery, the patient is alive and well. Postoperative imaging studies performed six months after surgery showed normal right kidney and no evidence of metastases in lungs, liver and the abdominal organs. There was no evidence of para-aortic lymphadenopathy or ascites.
Supporting Medical Planning by Mitigating Cognitive Load

Summary Objectives : Developing a care plan for a patient is a complex task, requiring an understanding of interactions and dependencies between procedures and of their possible outcomes for an individual patient. Decision support for planning has broader requirements than are typically considered in medical informatics applications. We consider the appropriate design of software to assist medical planning. Methods : The likely cognitive loads imposed by planning tasks were assessed with a view to directly supporting these via software. Results : Five types of cognitive load are likely to be important. A planning support system, REACT, was designed to ameliorate these cognitive loads by providing targeted dynamic feedback during planning. An initial evaluation study in genetic counselling indicates that the approach is successful in that role. Conclusions : The approach provides the basis of a general aid for visualizing, customizing and evaluating care plans.
Recent Developments in Multianalyte Immunoassay

Multianalyte immunoassay has gained increasing attention due to its high sample throughput, short assay time, low sample consumption and reduced overall cost per assay. Most of the current developed approaches for multianalyte immunoassay are based on spatial-resolved, multilabel or separation mode. This paper reviews the progress of multianalyte immunoassay and its applications in different fields with 90 references. The outlook of this promising technique has been discussed.
Virtual reality for mobility devices: training applications and clinical results: a review

Virtual reality technology is an emerging technology that possibly can address the problems encountered in training (elderly) people to handle a mobility device. The objective of this review was to study different virtual reality training applications as well as their clinical implication for patients with mobility problems. Computerized literature searches were performed using the MEDLINE, Cochrane, CIRRIE and REHABDATA databases. This resulted in eight peer reviewed journal articles. The included studies could be divided into three categories, on the basis of their study objective. Five studies were related to training driving skills, two to physical exercise training and one to leisure activity. This review suggests that virtual reality is a potentially useful means to improve the use of a mobility device, in training one's driving skills, for keeping up the physical condition and also in a way of leisure time activity. Although this field of research appears to be in its early stages, the included studies pointed out a promising transfer of training in a virtual environment to the real-life use of mobility devices.
Unrecognised Structural Implications of Casemix Management

This paper takes issue with some conceptual and hence practical shortcomings which underlie current attempts to use casemix methodologies in bringing medical clinicians within the writ of management. The reform programme is grounded in an instrumental conception of organisation which construes the conduct and structuring of relationships in a hospital as being the product of its alleged purposive character and its formal design features. Accordingly, it is assumed that improving hospital efficiency and effectiveness requires no more than recasting formal authority structures and introducing information systems which will extend management's capacity to surveil and control the performance of clinical work. The paper argues that this conception of hospital organisation and what is required to achieve reform, ignores institutional prerequisites which underpin management in industrial and commercial settings and denies evidence about a range of factors inherent in the prevailing organisation of medicine which militate against efforts to extend the writ of management over hospital-based medical work.