Miracle-dz/UniFAR-FTUs huggingface dataset:
Motion correction for improved target localization with on-board cone-beam computed tomography

On-board imager (OBI) based cone-beam computed tomography (CBCT) has become available in radiotherapy clinics to accurately identify the target in the treatment position. However, due to the relatively slow gantry rotation (typically about 60 s for a full 360° scan) in acquiring the CBCT projection data, the patient's respiratory motion causes serious problems such as blurring, doubling, streaking and distortion in the reconstructed images, which heavily degrade the image quality and the target localization. In this work, we present a motion compensation method for slow-rotating CBCT scans by incorporating into image reconstruction a patient-specific motion model, which is derived from previously obtained four-dimensional (4D) treatment planning CT images of the same patient via deformable registration. The registration of the 4D CT phases results in transformations representing a temporal sequence of three-dimensional (3D) deformation fields, or in other words, a 4D model of organ motion. The algorithm was developed heuristically in two-dimensional (2D) parallel-beam geometry and extended to 3D cone-beam geometry. By simulations with digital phantoms capable of translational motion and other complex motion, we demonstrated that the algorithm can reduce the motion artefacts locally, and restore the tumour size and shape, which may thereby improve the accuracy of target localization and patient positioning when CBCT is used as the treatment guidance.
La désinflation manquante : un phénomène américain uniquement ?

Le comportement de l’inflation aux Etats-Unis lors de la crise economique de 2008-2009, qui n’a pas suivi les predictions d’une courbe de Phillips classique, a donne lieu au phenomene de « missing disinflation ». Nous evaluons si ce phenomene a egalement eu lieu en zone euro. Nous trouvons que l’inflation en zone euro a bien suivi les predictions d’une courbe de Phillips, mais qu’il existe de fortes divergences intra-europeennes, entre d’un cote l’Allemagne et la France, ou l’inflation predite par une courbe de Phillips est proche de l’inflation realisee, et d’un autre l’Italie, l’Espagne et la Grece, ou dans la periode qui precede la crise financiere, l’inflation observee n’est pas en ligne avec l’inflation predite. La crise de 2009 semble avoir reduit partiellement ces deviations.
Online natural language processing of the Slovak Language

The Slovak NLP Demo should provide overview of the state-of-the-art NLP tools where each single processing step can be tried with arbitrary text, results can be reviewed and feedback can be sent to the authors. The demo is accessible on a web site, arbitrary text can be inserted using a form. Processing tools can be selected and processed text will be displayed. The web site contains additional resources, such as datasets, other tools and bibliographical information.
miRNA analysis in pancreatic cancer: the Dartmouth experience

Abstract: Pancreatic cancer is considered one of the most lethal cancers being the fourth leading cause of cancer deaths in adults in the United States because of the lack of early signs and symptoms and the lack of early detection. Pancreatic ductal adenocarcinoma (PDAC) is the most common histological type among pancreatic cancers, representing 80%–90% of all solid tumors of the pancreas. The majority of PDAC develops from three precursor lesions: pancreatic intraepithelial neoplasia, intraductual papillary mucinous neoplasm and mucinous cystic neoplasm. Although histologic tissue evaluation remains the gold standard for diagnosis, endoscopic ultrasound-guided fine needle aspiration has become the preferred modality for obtaining pathologic confirmation. At Dartmouth-Hitchcock Medical Center (DHMC),we have developed and validated a microRNA (miRNA) panel for patients with pancreatic diseases that can be used in association with the gold standard method for diagnosis. miRNAs have an important role in biological processes, such as apoptosis, metabolism, cell growth and differentiation. In cancer, miRNAs can be classified as either oncogenic or tumor suppressor according to their function in the carcinogenic process. In this study, we describe the expression of many miRNA in benign and malignant pancreatic tissues as well as their clinical significance. For this reason, miRNAs have been considered potential biomarkers of pancreatic diseases that could potentially contribute to an early diagnosis, predict disease progression, accurately monitor disease, contribute to better treatment strategies and reduce mortality by improving disease management.
Immunocytochemical detection of isolated epithelial cells in bone marrow: non‐specific staining and contribution by plasma cells directly reactive to alkaline phosphatase

Detection of isolated tumour cells (TCs) in bone marrow (BM) from epithelial cancer patients by immunocytochemical (ICC) analysis seems to predict future relapse, but the reported percentages of positive BMs among patients with localized cancer show large variations and the number of detected TCs is low. This emphasizes the importance of thoroughly testing the methods in use. This study was performed to clarify to what extent positive staining of haematopoietic cells (HCs) interferes with the ICC detection of epithelial cells in BM. BM mononuclear cells (MNCs) from normal donors and stage I–II breast cancer patients were stained with anti‐cytokeratin (CK) and isotype control monoclonal antibodies (MAbs) followed by alkaline phosphatase (AP)‐based visualization of immunolabelled cells. In the ICC staining of normal donors by the anti‐CK MAbs AE1/AE3 or A45‐B/B3, rare immunoreactive cells were detected in 7/20 and 8/19 BMs, respectively. Morphological examination recognized all these cells as typical HCs. In the breast cancer patients (n=257), anti‐CK‐positive cells were detected in 26·6 per cent, excluding cells with HC morphology. Using the same morphological criteria, isotype control‐positive cells were detected in 5·4 per cent of patients. Some of the false‐positive events were further analysed and cells with strong reactivity against the AP enzyme alone were detected. Double ICC staining recognized the majority of these AP directly‐reactive cells as CD45‐negative and human Ig kappa/lambda‐positive, in accordance with the phenotype of mature plasma cells. Morphological evaluation and adequate controls are important to ensure the diagnostic specificity of micrometastases in BM. It is recommended that the number of BM MNCs included in negative controls should equal the number of cells in the diagnostic specimens. © 1998 John Wiley & Sons, Ltd.
Impact of Risk Information on Perceived Colorectal Cancer Risk

The study sought to modify comparative optimism about colorectal cancer in a community sample using a method of providing risk information found to be effective in a laboratory setting. The 3185 adults from General Practice lists were randomized to three groups: (1) control—no information; (2) risk information leaflet; (3) risk and screening information leaflet. Significant comparative optimism and high numeric estimates of absolute risk were found. Risk factor information did not reduce optimistic beliefs nor modify estimates of risk. Interest in screening was high overall and not influenced by the information. Comparatively optimistic risk perceptions appear resistant to change in community settings.
Recovery of Acid Production in Streptococcus mutans Biofilms after Short-Term Fluoride Treatment

Fluoride is commonly used as an ingredient of topical oral hygiene measures. Despite the anti-acidogenic activities of fluoride against cariogenic biofilms, the recovery of the biofilms from fluoride damage is unclear. Herein, we investigated the recovery of acid production in Streptococcus mutans biofilms after short-term or during periodic 1-min fluoride treatments. For this study, 46-hour-old S. mutans biofilms were treated with fluoride (0-2,000 ppm F-) for 1-8 min and then incubated in saliva for 0-100 min. The 74-hour-old biofilms were also periodically treated with the fluoride concentration during biofilm formation (1 min/treatment). Changes in acidogenicity and viability were determined via pH drop and colony-forming unit assays, respectively. In this study, acid production after a 1-min fluoride treatment was recovered as saliva incubation time increased, which followed a linear pattern of concentration dependence (R = 0.99, R2 = 0.98). The recovery pattern was in a biphasic pattern, with an initial rapid rate followed by a second slow recovery. Furthermore, recovery from fluoride damage was retarded in a concentration-dependent manner as treatment time increased. In periodic 1-min fluoride treatments, acid production in the biofilms was not diminished during the non-fluoride treatment period; however, it was reduced in a concentration-dependent manner during the fluoride treatment period. The viability of the biofilm cells did not change, even at high fluoride concentrations. Collectively, our results suggest that brief fluoride treatment does not sustain anti-acidogenic activity against S. mutans in biofilms since the damage is recoverable with time.
FDG-PET-Detected Extracranial Metastasis in Patients with Non-Small Cell Lung Cancer Undergoing Staging for Surgery or Radical Radiotherapy

The prognostic significance of extracranial distant metastasis detected by positron emission tomography (PET) was investigated in patients with non-small cell lung cancer (NSCLC). Forty-two patients staged with 18 F-fluorodeoxyglucose-PET-detected distant metastasis before planned surgery (n=7) or radical radiotherapy (RT)/chemoradiotherapy (n=35) for NSCLC were identified from a prospective database. The influence of metastasis number and other prognostic factors was investigated using Cox's regression analysis. Treatment after PET included surgery (n=2), radical RT (n =5), palliative RT (n=25), chemotherapy (n=8) or supportive care (n=2). All but 4 patients had died by the last follow-up. Median survival was 9 months overall, 12 months for 27 patients with single PET-detected metastasis and 5 months for 15 patients with >1 metastasis (p=0.009). It was found that the Eastern Cooperative Oncology Group performance status (p=0.027) but not pre-PET stage, weight loss or metastasis site correlated with survival. PET-detected metastatic tumor burden appeared to influence survival and should be evaluated as a prognostic factor in NSCLC.
Full Adder Cell for Low Power Arithmetic Applications

Arithmetic circuits like adder, multiplexer etc. arethe most important circuits in digital signal processing andmany more applications. Full adder circuit is the basic cell ofarithmetic circuits. Many applications require circuits of highthroughput, small area and consume ultra-low power. In thisregards, this paper brings forward a new full adder circuitthat uses 10-Transistors and improved version of the proposed circuit. This full adder uses low power XOR gates to generate sum signal and a multiplexer of two transistors, to generate carry out signal. Generic Process Design Kit (GPDK) 45nm technology is employed in Cadence virtuoso design environment to design circuits which are simulated with Spectre simulator.
Weighted gene co-expression network analysis of colorectal cancer liver metastasis genome sequencing data and screening of anti-metastasis drugs

After the publication of the article, the authors noted that the affiliation for Dr Hani Choudhry is wrong. The correct affiliation should be as follows: Bo Gao1, Qin Shao2, Hani Choudhry3, Victoria Marcus2, Kung Dong5, Jiannis Ragoussis4 and Zu-Hua Gao2, 1Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China; 2Department of Pathology, The Research Institute of McGill University Health Center, Montreal, Québec H4A 3J1, Canada; 3Department of Biochemistry, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia; 4McGill University and Genome Quebec Innovation Centre, Montreal, Québec H3B 1S6, Canada; 5Department of Pathology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P.R. China. [the original article was published in the International Journal of Oncology 49: 1108-1118, 2016; DOI: 10.3892/ijo.2016. 3591].
Predicting potential survival benefit of renal transplantation in patients with chronic kidney disease

Background: To facilitate decision-making about treatment options for patients with end-stage renal disease considering kidney transplantation, we sought to develop an index for clinical prediction of risk for death. Methods: We derived and validated a multivariable survival model predicting time to death in 169 393 patients with end-stage renal disease who were eligible for transplantation. We modified the model into a simple point-system index. Results: Deaths occurred in 23.5% of the cohort. Twelve variables independently predicted death: age, race, cause of kidney failure, body mass index, comorbid disease, smoking, employment status, serum albumin level, year of first renal replacement therapy, kidney transplantation, time to transplant wait-listing and time on the wait list. The index separated patients into 26 groups having significantly unique five-year survival, ranging from 97.8% in the lowest-risk group to 24.7% in the highest-risk group. The index score was discriminative, with a concordance probability of 0.746 (95% CI 0.741–0.751). Observed survival in the derivation and validation cohorts was similar for each level of index score in 93.9% of patients. Interpretation: Our prognostic index uses commonly available information to predict mortality accurately in patients with end-stage renal disease. This index could provide valuable quantitative data on survival for clinicians and patients to use when deciding whether to pursue transplantation or remain on dialysis.
The Induction and Refresher scheme Simulated Surgery

The Induction and Refresher scheme Simulated Surgery (I&RSS) is an assessment of clinical and consulting skills in which candidates are observed consulting with a series of simulated patients who present a variety of common GP scenarios. The Committee of GP Education Directors (COGPED) recommends a period of induction for GPs returning to practice after a time away and GPs from the European Union wishing to enter UK general practice. In some deaneries the Induction and Refresher scheme is also the means by which GPs with fitness to practise concerns can be remediated back into the workplace. The I&RSS is used by English deaneries to assess their learning needs prior to entry into the scheme. This paper describes the I&RSS and its validity and reliability. We explain how it differs from the MRCGP Clinical Skills Exam and how it provides formative feedback to candidates. We report on the outcomes of the exam for the last two years and discuss the performance of different candidate groups.
Structure and monomer/dimer equilibrium for the guanylyl cyclase domain of the optogenetics protein RhoGC

RhoGC is a fusion protein from the aquatic fungus Blastocladiella emersonii, combining a type I rhodopsin domain with a guanylyl cyclase domain. It has generated excitement as an optogenetics tool for the manipulation of cyclic nucleotide signaling pathways. To investigate the regulation of the cyclase activity, we isolated the guanylyl cyclase domain from Escherichia coli with (GCwCCRho) and without (GCRho) the coiled-coil linker. Both constructs were constitutively active but were monomeric as determined by size-exclusion chromatography and analytical ultracentrifugation, whereas other class III nucleotidyl cyclases are functional dimers. We also observed that crystals of GCRho have only a monomer in an asymmetric unit. Dimers formed when crystals were grown in the presence of the non-cyclizable substrate analog 2′,3′-dideoxyguanosine-5′-triphosphate, MnCl2, and tartrate, but their quaternary structure did not conform to the canonical pairing expected for class III enzymes. Moreover, the structure contained a disulfide bond formed with an active-site Cys residue required for activity. We consider it unlikely that the disulfide would form under intracellular reducing conditions, raising the possibility that this unusual dimer might have a biologically relevant role in the regulation of full-length RhoGC. Although we did not observe it with direct methods, a functional dimer was identified as the active state by following the dependence of activity on total enzyme concentration. The low affinity observed for GCRho monomers is unusual for this enzyme class and suggests that dimer formation may contribute to light activation of the full-length protein.
Timing Functions of The Cerebellum

This study investigated the effects of different types of neurological deficits on timing functions. The performance of Parkinson, cerebellar, cortical, and peripheral neuropathy patients was compared to age-matched control subjects on two separate measures of timing functions. The first task involved the production of timed intervals in which the subjects attempted to maintain a simple rhythm. The second task measured the subjects' perceptual ability to discriminate between small differences in the duration of two intervals. The primacy of the cerebellum in timing functions was demonstrated by the finding that these were the only patients who showed a deficit in both the production and perception of timing tasks. The cerebellar group was found to have increased variability in performing rhythmic tapping and they were less accurate than the other groups in making perceptual discriminations regarding small differences in duration. Critically, this perceptual deficit appears to be specific to the perception of time since the cerebellar patients were unaffected in a control task measuring the perception of loudness. It is argued that the operation of a timing mechanism can be conceptualized as an isolable component of the motor control system. Furthermore, the results suggest that the domain of the cerebellar timing process is not limited to the motor system, but is employed by other perceptual and cognitive systems when temporally predictive computations are needed.
Improved insulin sensitivity after weight loss and exercise training is mediated by a reduction in plasma fatty acid mobilization, not enhanced oxidative capacity

Obesity is characterized by excessive rates of plasma fatty acid mobilization and uptake, which play a key role in mediating insulin resistance. While weight loss via diet‐only or a diet + exercise program clearly improves insulin sensitivity, the precise mechanisms modulating this improvement are not completely understood. The purpose of the present study was to determine the role of the reduced fatty acid mobilization and uptake after weight loss in obese women who were randomly assigned to lifestyle interventions of either weight loss without exercise (WL) (n= 7) or a weight loss + exercise program (WL + EX) (n= 10). Before and after losing 12% of their body weight, we measured insulin sensitivity (SI), systemic fatty acid rate of appearance (Ra) and disappearance (Rd), oxidative capacity, and markers for pro‐inflammatory pathways in skeletal muscle. Fatty acid Ra and Rd were reduced by ∼30% after both interventions (P < 0.05). While oxidative capacity increased 25% in WL + EX (compared with no increase after WL), the improvement in SI was identical in both groups (∼60%; P < 0.05), and skeletal muscle pro‐inflammatory pathways were reduced (P < 0.05) similarly in both groups. When we artificially increased fatty acid mobilization after weight loss to pre‐weight‐loss levels via an overnight lipid infusion, the improvement in SI was almost completely reversed. Importantly, WL + EX did not protect against this lipid‐induced reversal in SI despite a significant increase in resting whole‐body fat oxidation and a marked increase in skeletal muscle oxidative capacity. In conclusion, reduced fatty acid mobilization and uptake appears to be a primary mediator of improved insulin sensitivity after weight loss. Moreover, enhancing fatty acid oxidative capacity via exercise training is not sufficient to prevent the insulin resistance caused by high fatty acid mobilization, such as that found in obesity.
Estimation of respiratory waveform and heart rate using an accelerometer

In this paper the use of an accelerometer to measure cardio-respiratory activity is presented. Movement of the chest was recorded by an accelerometer attached to a belt around the chest. The acquisition is realized in different status: normal, apnea, deep breathing or after exhaustion and also in different postures: vertical (sitting, standing) or horizontal (lying down). The resulting signal was compared with reference measurements. The results of experimental evaluation indicate that using a chest-accelerometer can correctly detect the respiratory waveform and heart rate (HR) signal. This method is therefore suitable for automatic identification some disease, for example arrhythmia or sleep apnea.
Paroxetine hydrochloride hemihydrate.

The structure of the title compound {systematic name: (3S-trans)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4- fluorophenyl)piperidinium chloride hemihydrate, C19H21FNO3+. Cl-. 0.5H2O}, comprises two piperidinium cations (A and B), two chloride anions, and one water molecule in the asymmetric unit. A piperidinium proton of cation A is hydrogen bonded to the water molecule. The second proton points in the direction of one chloride anion, as does a piperidinium proton of cation B. One water proton points in the direction of another chloride anion.
Sonic hedgehog from pharyngeal arch 1 epithelium is necessary for early mandibular arch cell survival and later cartilage condensation differentiation

Background: Morphogenesis of vertebrate craniofacial skeletal elements is dependent on a key cell population, the cranial neural crest cells (NCC). Cranial NCC are formed dorsally in the cranial neural tube and migrate ventrally to form craniofacial skeletal elements as well as other tissues. Multiple extracellular signaling pathways regulate the migration, survival, proliferation, and differentiation of NCC. Results: In this study, we demonstrate that Shh expression in the oral ectoderm and pharyngeal endoderm is essential for mandibular development. We show that a loss of Shh in these domains results in increased mesenchymal cell death in pharyngeal arch 1 (PA1) after NCC migration. This increased cell death can be rescued in utero by pharmacological inhibition of p53. Furthermore, we show that epithelial SHH is necessary for the early differentiation of mandibular cartilage condensations and, therefore, the subsequent development of Meckel's cartilage, around which the dentary bone forms. Nonetheless, a rescue of the cell death phenotype does not rescue the defect in cartilage condensation formation. Conclusions: Our results show that SHH produced by the PA1 epithelium is necessary for the survival of post‐migratory NCC, and suggests a key role in the subsequent differentiation of chondrocytes to form Meckel's cartilage. Developmental Dynamics 244:564–576, 2015. © 2015 Wiley Periodicals, Inc.