Miracle-dz/UniFAR-FTUs huggingface dataset:
Urinary bladder cancer: diffusion-weighted MR imaging--accuracy for diagnosing T stage and estimating histologic grade.

PURPOSE To prospectively evaluate the ability of diffusion-weighted (DW) magnetic resonance (MR) imaging to be used to determine the T stage of bladder cancer and to measure the correlation between the apparent diffusion coefficient (ADC) and histologic grade. MATERIALS AND METHODS This study was approved by the local institutional review board. All patients gave written informed consent. Forty patients with a total of 52 bladder tumors underwent MR imaging that included DW imaging. Histologic grade was determined for all tumors. Two radiologists interpreted four image sets (ie, T2-weighted images alone, T2-weighted plus DW images, T2-weighted plus dynamic contrast agent-enhanced images, all three image types together). Conventional criteria were used for interpreting T2-weighted and contrast-enhanced images. For DW images, new staging criterion developed on the basis of the hypothesis that tumors, submucosal tissue, and muscles show high, low, and intermediate signal intensity, respectively, was used. The McNemar test was used to examine differences in accuracy, sensitivity, and specificity. Differences in the performance were analyzed by comparing the areas under the receiver operating characteristic curves (A(z) values). To compare ADCs between three histologic grades, analysis of variance was used. RESULTS The overall accuracy of T stage diagnosis was 67% for T2-weighted images alone, 88% for T2-weighted plus DW images, 79% for T2-weighted plus contrast-enhanced images, and 92% for all three image types together. The overall accuracy, specificity, and A(z) for diagnosing T2 or higher stages were significantly improved by adding DW images (P < .01). The mean ADC of G3 tumors was significantly lower than that of G1 and G2 tumors (P < .01). CONCLUSION DW images provided useful information for evaluating the T stage of bladder cancer, particularly in differentiating T1 or lower tumors from T2 or higher tumors. The ADC may in part predict the histologic grade of bladder cancer.
Molecular Query Language (MQL)A Context-Free Grammar for Substructure Matching

We have developed a Java library for substructure matching that features easy-to-read syntax and extensibility. This molecular query language (MQL) is grounded on a context-free grammar, which allows for straightforward modification and extension. The formal description of MQL is provided in this paper. Molecule primitives are atoms, bonds, properties, branching, and rings. User-defined features can be added via a Java interface. In MQL, molecules are represented as graphs. Substructure matching was implemented using the Ullmann algorithm because of favorable run-time performance. The Ullmann algorithm carries out a fast subgraph isomorphism search by combining backtracking with effective forward checking. MQL software design was driven by the aim to facilitate the use of various cheminformatics toolkits. Two Java interfaces provide a bridge from our MQL package to an external toolkit: the first one provides the matching rules for every feature of a particular toolkit; the second one converts the found match from the internal format of MQL to the format of the external toolkit. We already implemented these interfaces for the Chemistry Development Toolkit.
On-line venous oxygen tensions in rainbow trout during graded exercise at two acclimation temperatures

SUMMARY For most teleost fish, the majority of the myocardial oxygen supply is provided by the oxygen reserve remaining in venous blood after other tissues have extracted oxygen. We examined the effect of graded exercise and water temperature on this venous blood oxygen supply to the heart (termed the cardiac circulation) by performing novel on-line measurements of venous partial pressure of oxygen (PvO2) using a fibreoptic micro-optode implanted in the ductus Cuvier of rainbow trout (Oncorhynchus mykiss). As expected, PvO2 decreased progressively and significantly as swimming velocity approached the critical swimming speed (Ucrit). Unsteady swimming behaviours during the graded exercise, however, caused abrupt and generally short-lived decreases in PvO2. For the cold-acclimated (6-10°C) fish, PvO2 reached a minimum plateau value of 15.3±3.7 torr (1 torr=133.3 Pa) before Ucrit was reached, and so increased swimming effort near to Ucrit did not reduce PvO2 further. Warm-acclimated fish had a significantly higher PvO2 (28.9±3.5 torr) at Ucrit. Despite this difference in the PvO2 at Ucrit, we estimated that there was little difference between warm- and cold-acclimated fish in terms of oxygen supply in the cardiac circulation because of a right-shift in the haemoglobin—oxygen dissociation curve at warm temperatures. Furthermore, although PvO2 decreased significantly at Ucrit, our estimates suggest that the expected increase in cardiac output would easily maintain the oxygen supply in venous blood at a level similar to that found in resting fish. Although unsteady swimming behaviours decreased PvO2, unsteady swimming rarely decreased the minimum PvO2 value observed at Ucrit by more than 10%. The findings are discussed in terms of a threshold PvO2 required to maintain adequate rates of oxygen diffusion from the cardiac circulation to the myocardial tissues.
Public housing in Australia is in decline: The facts speak for themselves

This article is a brief statistical overview of the decline in the capacity of the public housing system using figures presented in the Commonwealth government Housing Assistance Act reports. It does not provide extensive analysis as this is contained in other articles in this publication. There is a range of statistical sources regarding public housing all suggesting, in various ways a broad decline in housing stock.
Familial Creutzfeldt-Jakob Disease Presenting with Subacute Multiple Cranial Neuropathy

Unusual clinical presentations in patients with E200K familial Creutzfeldt-Jakob Disease (fCJD) have been rarely reported. Herein, we described a case of E200K fCJD presenting with subacute cranial multiple neuropathy, initially suspected to be paraneoplastic or due to a leptomeningeal carcinomatosis, considering the neoplastic comorbidity of the patient. Surprisingly, brain MRI was highly suggestive of CJD. Brain histological examination confirmed the diagnosis. Genetic tests led to the definite diagnosis of E200K fCJD. To the best of our knowledge, the current case provides the first report of a histologically-confirmed E200K fCJD starting with cranial multiple neuropathy and may widen the spectrum of the clinical variability of CJD, also in its genetic variant. Unusual presentations may lead, as in this case, to incorrect diagnostic hypothesis and unuseful therapeutic attempts in the first phase of the diagnostic process. Also in the genetic variant of CJD, brain MRI demonstrated a very high sensitivity to detect the typical abnormalities since the earliest phases of the disease.
Efficacy of adoptive immunotherapy with donor lymphocyte infusion in relapsed lymphoid malignancies.

AIMS There is a perceived benefit associated with the administration of donor lymphocyte infusion (DLI) in patients with lymphoid malignancies relapsing after allogeneic hematopoietic cell transplantation. However, it is unclear if and how this benefit varies according to specific diseases. Because administration of DLI is not universally effective and could be associated with significant toxicities resulting in morbidity and mortality, it is imperative to identify cases where benefits outweigh harms of the procedure. MATERIALS & METHODS We conducted a systematic review of the published literature and extracted and pooled data independently for each disease cohort: acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), multiple myeloma (MM), non-Hodgkin's lymphoma (NHL) and Hodgkin's lymphoma (HL). RESULTS In summary, 39 studies met inclusion criteria. The pooled proportion (95% CI) for complete response was 27% (16-40) in ALL, 55% (15-92) in CLL, 26% (19-33) in MM, 52% (33-71) in NHL and 37% (20-56) in HL. CONCLUSION Complete response rates appear higher when DLI is used for relapsed CLL and lymphomas (NHL and HL), and less pronounced in ALL or MM. Absence of data pertaining to disease-specific prognostic determinants, such as adverse genetic or molecular abnormalities, or quantitative disease burden when applicable, limit our ability to identify cases in whom benefits from DLI outweigh risks associated with the procedure within a particular disease.
BIDDING FOR OLD AND NEW BUSINESS

The telephone of just-reelected New Frankfurt mayor Gus Karloff has been ringing incessantly since the story broke. Three days ago, the New Frankfurt Publius reported that Gary Goldstein, the CEO of BioNew, had lunched with a local real estate developer. The newspaper also reported that BioNew's five-year plan includes opening a new site in the American Southeast. BioNew, a Fortune 500 biotechnology firm, was started by Gary Goldstein in 1984. In 19 years, the company went from having six employees in one location to having 1,302 employees in three locations. The majority of BioNew's operations are in the New York/New Jersey SMSA. BioNew is a pioneer in the area of pharmaceutical discovery and development. The firm holds three patents and has applied for two more on pharmaceuticals designed to treat infections caused by RNA viruses. It is also rumored that BioNew has a new pharmaceutical in research and development that could address some of the secondary infections of HIV. In November, BioNew management held a press conference to announce that they are looking to expand into new areas that focus on pharmaceuticals that deal with Parkinson's disease as well as spinal cord injuries.
Long-term dynamics of water-borne nitrogen, phosphorus and suspended solids in the lower Don River basin (Russian Federation)

A long-term study (1986–2002) of water-borne nutrient and suspended solids dynamics was undertaken on the lower Don River, which plays an extremely important role in the water supply of the Black Sea and Azov Sea basin. Suspended solids were greatest in spring and summer and were correlated to river discharge. Mean annual nitrogen concentrations increased from 1986 to 1995 and then decreased from 1996 to 2002. Unlike nitrogen, phosphorus concentrations (both phosphates and total phosphorus) gradually increased throughout the study period changing the river from an oligotrophic to upper mesotrophic status. If this trend continues phytoplankton could become nitrogen-limited leading to the development of nitrogen-fixing cyanobacterial blooms. No obvious relation between fertiliser usage over the Rostovskaya Oblast and nutrient dynamic patterns was identified, probably because only 10% of the water in the river comes from this area. The reason for the unusual and contradictory nitrogen and phosphorus changes remain largely unknown for this regulated river.
Principles of the Exclusive Muddle

This paper provides a lexical entry schema for exclusives covering the adverbs only, just, exclusively, merely, purely, solely, simply, and the adjectives only, sole, pure, exclusive and alone. We argue, on the basis of inter-paraphrasability relations among these exclusives and entailments involving at least and at most, that all of these items make an at-issue contribution of an upper bound on the viable answers to the current question under discussion (expressible with at most), and signal that a lower bound on those answers (expressible with at least) is taken for granted. The lexical entry schema accommodates two main points of variation, which makes it possible to capture the differences in meaning among these terms: (i) semantic type (restricted to the class of modifiers), and (ii) constraints on the current question under discussion or the strength ranking over its alternative possible answers. We propose 22 different specific instantiations of the schema for exclusives in English.
Dancing with different partners: protein kinase a phosphorylation of seven membrane-spanning receptors regulates their G protein-coupling specificity.

In simpler times, studies of G protein-coupled receptor (GPCR) signaling focused almost exclusively on pathways characterized by a small number of sequential events, largely confined to the plasma membrane [for example, activation of adenylyl cyclase by the β2AR ([Lefkowitz, 2000][1])]. However, in
Secret Image Hiding and Sharing Based on the (t, n)-Threshold

This study proposes a new secret image sharing method based on the (t,n)-threshold. The sharing method is completed through three main steps: (1) quantizing the secret image, (2) generating n shadows from the quantized image, and (3) sharing the n shadows among n cover images. Our goal is both to attain good stego-image and secret image quality preservation effects and to limit the size of each shadow image down to 1/t of that of the secret image for convenient transmission and storage. In the first step, the secret image is divided into non-overlapping 4 × 4 blocks that are quantized according to the results of block testing. Each block, after the block testing procedure, is judged to be either a smooth block or a non-smooth one. Smooth blocks can be neatly restored after being hidden into the cover image, while non-smooth blocks can be somewhat lossy, but such modification is perceptually invisible. The second step is to apply Shamir's (t,n)-threshold, which uses a (t−1)-degree polynomial to generate n shadows so that the secret image can be restored from any t out of n shadows. The last step involves a modulo operation to hide the n shadows in n cover images. According to our experimental results, the PSNR values of the reconstructed secret images by our method center around 39 dB, outperforming other recent methods.
Quality Control of Photosystem II

The reaction center-binding D1 protein of Photosystem II is oxidatively damaged by excessive visible light or moderate heat stress. The metalloprotease FtsH has been suggested as responsible for the degradation of the D1 protein. We have analyzed the distribution and subunit structures of FtsH in spinach thylakoids and various membrane fractions derived from the thylakoids using clear native polyacrylamide gel electrophoresis and Western blot analysis. FtsH was found not only in the stroma thylakoids but also in the Photosystem II-enriched grana membranes. Monomeric, dimeric, and hexameric FtsH proteases were present as major subunit structures in thylakoids, whereas only hexameric FtsH proteases were detected in Triton X-100-solubilized Photosystem II membranes. Importantly, among the membrane fractions examined, hexameric FtsH proteases were most abundant in the Photosystem II membranes. In accordance with this finding, D1 degradation took place in the Photosystem II membranes under light stress. Sucrose density gradient centrifugation analysis of thylakoids and the Photosystem II membranes solubilized with n-dodecyl-β-d-maltoside and a chemical cross-linking study of thylakoids showed localization of FtsH near the Photosystem II light-harvesting chlorophyll-protein supercomplexes in the grana. These results suggest that part of the FtsH hexamers are juxtapositioned to PSII complexes in the grana in darkness, carrying out immediate degradation of the photodamaged D1 protein under light stress.
Coinfection of a Bearded Dragon, Pogona vitticeps, with Adenovirus- and Dependovirus-like Viruses

Four neonate bearded dragons, Pogona vitticeps, from two collections became ill and died. Multiple tissues were collected and processed for light microscopy. In hematoxylin and eosin-stained sections of liver of one lizard, numerous basophilic intranuclear inclusions were observed. In three lizards, intranuclear inclusions were primarily seen within enterocytes in the small intestine. A portion of paraffin-embedded liver of one lizard and small intestine of a second lizard were removed, deparaffinized, and examined by electron microscopy. For the most part, inclusions in the liver consisted of nonenveloped viral particles 60-66 nm in diameter. Smaller nonenveloped virions 15-17 nm in diameter were occasionally seen in association with these particles. In the intestine, inclusions consisted only of 60-70 nm particles. Based on morphology and location, the larger particles were consistent with an adenovirus. Based on size and presence within nuclei of host cells coinfected with the adenovirus-like virus, the smaller viral agent was consistent with members of the genus Dependovirus.
Altered gene expression correlates with DNA structure.

We examined the participation of triplex DNA structure in gene regulation using a poly(dG)-poly(dC) sequence as a model. We show that a poly(dG)-poly(dC) sequence, which can adopt an intramolecular dG.dG. dC triplex under superhelical strain, strongly augments gene expression when placed 5' to a promoter. The activity of this sequence exhibits a striking length dependency: dG tracts of 27-30 bp augment the expression of a reporter gene to a level comparable to that observed with the polyoma enhancer in mouse LTK- cells, whereas tracts of 35 bp and longer have virtually no effect. A supercoiled plasmid containing a dG tract of 30 bp competes in vivo for a trans-acting factor as revealed by reduction in the reporter gene transcription driven by the (dG)29/promoter of the test plasmid, while dGs of 35 bp and longer in the competition plasmid failed to compete. In purified supercoiled plasmid DNA at a superhelical density of -0.05, dG tracts of 32 bp and longer form a triplex, whereas those of 30 bp and shorter remain double-stranded under a PBS solution. These results suggest that a localized superhelical strain can exist, at least transiently, in mouse LTK- cells, and before being relaxed by topoisomerases this rapidly induces dG tracts of 35 bp and longer to adopt a triplex preventing the factor from binding. Thus, these data suggest that a poly(dG)-poly(dC) sequence can function as a negative regulator by adopting an intramolecular triple helix structure in vivo.
Analysis of clinicopathologic factors in malignant mixed Müllerian tumors of the uterine corpus

The aim of this study was to retrospectively analyze the clinical and pathologic data of a series of patients presenting to our unit with uterine malignant mixed Müllerian tumors (MMMT) to attempt to identify prognostic factors and relate them to survival. Thirty-seven patients diagnosed with MMMT of the uterus from 1988 through 2000 were identified from the gynecological tumor registry. Data was abstracted and analyzed. The effect of a variety of clinical, histopathologic, and surgical variables on recurrence and survival were analyzed by univariate and multivariate analyses. Patients tended to be postmenopausal, overweight, hypertensive, and presented with abnormal bleeding. Preoperatively 28 (76%) were thought to have clinical stage I-II disease. Nine (32%) were upstaged based on surgical data. Five (56%) of these patients were found to have gross extrauterine disease and four (44%) were found subsequently to have microscopic extrauterine disease. Twenty (54%) patients underwent lymph node dissection and positive nodes were found in seven (35%) patients. Nine patients underwent omentectomy and disease was found in three (33%). Peritoneal washings were positive in three of 16 patients (19%). At the completion of primary surgery, 27 (75%) patients had no residual disease. Twelve (44%) of these patients had recurrence of disease. Median disease-free interval prior to first recurrence was 15 months. Median overall survival was 30 months. Log-rank analysis performed on multiple variables, including stage, age, residual disease, and depth of myometrial invasion showed a statistically significant association with overall survival probability. Only stage remained a significant independent variable predictive of overall survival (P = 0.034). We found that stage was an independent prognostic factor for overall survival in patients with uterine MMMT. Age, depth of myometrial invasion, and residual tumor were significant prognostic factors on univariate analysis. These factors may be a guide in order to select a group of high risk patients that may benefit from adjuvant therapy.
Interactive effects of contaminants and climate‐related stressors: High temperature increases sensitivity to cadmium

An emerging issue in environmental toxicology is in understanding how climate change will alter responses of organisms to chemical contaminants. The objective of the present study was to characterize the interactive effects of cadmium and elevated temperature on life‐stage‐specific responses in the freshwater snail Physa pomilia. We exposed developing eggs, juveniles, and adults to Cd (5 µg/L, 15 µg/L, and 25 µg/L for eggs, and 250 µg/L for juveniles and adults) and 2 temperatures of 25 °C (control) and 35 °C (upper range of tolerance). In the absence of Cd, time to hatch was shorter at 35 °C compared with 25 °C, demonstrating a stimulatory effect of the higher temperature. However, when egg masses were reared at 35 °C and exposed to Cd, hatching success was significantly lower, and time‐to‐hatching was significantly longer. The effects of the higher temperature and Cd on newly hatched neonate survival were additive, except at the highest Cd concentration, at which effects of the 2 stressors were greater than additive. Overall, within the combined stressor treatments, adult snails generally survived significantly longer than did juvenile snails, and both were more tolerant than developing snails. Many climate projection models predict future increases in global temperatures. The present study shows that combined stressors may produce greater‐than‐additive effects, challenging predictive power. More studies are needed to better characterize the interactive effects of chemical contaminants and stressors related to climate change. Environ Toxicol Chem 2013;32:1337–1343. © 2013 SETAC
Inactivation of the phosphoglucomutase gene pgm in Corynebacterium glutamicum affects cell shape and glycogen metabolism

In Corynebacterium glutamicum formation of glc-1-P (α-glucose-1-phosphate) from glc-6-P (glucose-6-phosphate) by α-Pgm (phosphoglucomutase) is supposed to be crucial for synthesis of glycogen and the cell wall precursors trehalose and rhamnose. Furthermore, Pgm is probably necessary for glycogen degradation and maltose utilization as glucan phosphorylases of both pathways form glc-1-P. We here show that C. glutamicum possesses at least two Pgm isoenzymes, the cg2800 (pgm) encoded enzyme contributing most to total Pgm activity. By inactivation of pgm we created C. glutamicum IMpgm showing only about 12% Pgm activity when compared to the parental strain. We characterized both strains during cultivation with either glucose or maltose as substrate and observed that (i) the glc-1-P content in the WT (wild-type) and the mutant remained constant independent of the carbon source used, (ii) the glycogen levels in the pgm mutant were lower during growth on glucose and higher during growth on maltose, and (iii) the morphology of the mutant was altered with maltose as a substrate. We conclude that C. glutamicum employs glycogen as carbon capacitor to perform glc-1-P homeostasis in the exponential growth phase and is therefore able to counteract limited Pgm activity for both anabolic and catabolic metabolic pathways.