Miracle-dz/UniFAR-FTUs huggingface dataset:
Breast Papilloma without Atypia and Risk of Breast Carcinoma

The incidence of asymptomatic papilloma has increased with the rising popularity of core needle biopsy for breast lesions. In this study, the risk of benign papilloma without atypia for subsequent breast carcinoma during follow‐up was evaluated. From January 2000 to December 2010, among 39,461 women with breast ultrasonography, 37,847 women with benign papilloma on biopsy or excision, with benign diseases on biopsy, and with only ultrasonography performed were recruited. Women with concurrent or prior high‐risk lesions (atypia, phyllodes tumor, or lobular neoplasm) or malignancies, or with a follow‐up period of less than 12 months were excluded. The eligible 12,302 women were classified into three groups; papilloma (n = 265, patients with benign papilloma without atypia at excision), benign (n = 3,066, patients with benign results other than high risk results on core needle biopsy), and ultrasonography (n = 8,971, patients who underwent ultrasonography only without biopsy or surgery). The relative risks (RRs) of the papilloma and benign groups were calculated with intervals of 2 years using the Poisson regression analysis with age, family history, follow‐up period, and breast parenchymal density being adjusted, and the ultrasonography group was used as a reference. The RR of the papilloma group was 4.8 (95% confidence interval [CI], 2.5–9.0), significantly higher than 1.5 (95% CI, 1.0–2.1) of the benign group. In the first 2 years, the RR of the papilloma group was 5.2 (95% CI, 2.2–12.6) but it dropped to 2.2 (95% CI, 0.5–9.2) during the next 2 years. Afterward, the RR increased over time although statistical significance was not achieved. Benign papilloma without atypia increased breast cancer risk fivefold when the ultrasonography group was used as a reference, higher than other benign lesions.
Words Are More Than The Sum Of Their Parts: Evidence For Detrimental Effects Of Word-Level Information in Alexia

The effects of sequential letter presentation on reading were investigated with both normal readers and an alexic patient. Normal readers showed longer naming latencies when words were presented letter-by-letter than when all the letters were presented simultaneously. In contrast, naming latencies for the alexic reader were shorter when words were presented letter-by-letter (error rates did not differ for the patient and the controls). Further experiments provided evidence for the patient being abnormally affected by lateral masking between stimuli, though she could access phonology from subword functional spelling units. The experiments demonstrate that, for alexic and normal readers alike, words are more than the sum of their individual letters; however, for normal readers a supra-letter reading strategy is useful whereas it can be detrimental in alexia.
Histone deacetylases 1 and 2 are expressed at distinct stages of neuro‐glial development

The deacetylation of histone proteins, catalyzed by histone deacetylases (HDACs), is a common epigenetic modification of chromatin, associated with gene silencing. Although HDAC inhibitors are used clinically to treat nervous system disorders, such as epilepsy, very little is known about the expression pattern of the HDACs in the central nervous system. Identifying the cell types and developmental stages that express HDAC1 and HDAC2 within the brain is important for determining the therapeutic mode of action of HDAC inhibitors, and evaluating potential side effects. Here, we examined the expression of HDAC1 and HDAC2 in the murine brain at multiple developmental ages. HDAC1 is expressed in neural stem cells/progenitors and glia. In contrast, HDAC2 is initiated in neural progenitors and is up‐regulated in post‐mitotic neuroblasts and neurons, but not in fully differentiated glia. These results identify key developmental stages of HDAC expression and suggest transitions of neural development that may utilize HDAC1 and/or HDAC2. Developmental Dynamics 237:2256–2267, 2008. © 2008 Wiley‐Liss, Inc.
An Application of Lexical Semantics Annotation to Question-Answering in e-Farming

In this poster we present an approach to responding to complex questions in the agriculture domain, from specifications given by experts. We present in particular a semantic annotation procedure that would allow us to define accurate and domain dedicated forms of lexical semantics inference, in order to be able to match non factoid questions (i.e. questions whose response is a significant text portion) with documents on a large scale. This project is designed to help farmers to get advices via question answering on SMS in order to improve rice farming.
Impaired gist memory in patients with temporal lobe epilepsy and hippocampal sclerosis

Purpose: Temporal lobe epilepsy (TLE) is the most common focal epilepsy and frequently causes memory problems. It is often associated with hippocampal sclerosis (HS) and is useful in exploring memory functions. We aimed to examine the effect of restricted hippocampal lesions on gist memory function in patients with TLE.
Bacterial vaginosis: a critical analysis of current knowledge

Bacterial vaginosis (BV), the change from a Lactobacillus‐dominant vaginal microbiota to an anaerobic and facultative bacterial dominance, is associated with pathological sequelae. In many BV‐positive women their microbiota is in fact normal and unrelated to pathology. Whether or not the dominance of BV‐associated bacteria persists depends upon interactions between host and bacterial factors. Inconsistencies in diagnosis and erroneous associations with pathology may be due to a failure to differentiate between sub‐populations of women. It is only in those women with a BV diagnosis in which the identified bacteria are atypical and persist that BV may be a clinical problem requiring intervention.
Closing the Gaps: A Full Scan of the Intestinal Expression of P-Glycoprotein, Breast Cancer Resistance Protein, and Multidrug Resistance-Associated Protein 2 in Male and Female Rats

Intestinal ATP binding cassette (ABC) transporters may affect the bioavailability and effectiveness of orally administered drugs. Available studies on regional expression of intestinal efflux transporters were done with selected intestinal segments only and inconsistent with regard to the variability of transporter expression and the course of expression along the intestine. For an evaluation of the consistency between mRNA and protein expression, relative expression levels of P-glycoprotein (Pgp; ABCB1), breast cancer resistance protein (Bcrp; ABCG2), and multidrug resistance-associated protein (Mrp) 2 (ABCC2) were determined using quantitative real-time-polymerase chain reaction and Western blot in rat intestinal segments from duodenum, jejunum, ileum, and colon. In addition, the protein expression of Pgp, Bcrp, and Mrp2 from the entire rat intestine was studied by a complete 3-cm segmentation to evaluate the predictive power of expression analyses from selected intestinal segments. Pgp showed an increase from proximal to distal regions, Bcrp showed an arcuate pattern with highest expression toward the end of small intestine, and Mrp2 decreased along the intestinal axis from proximal to distal parts. No gender specific differences could be observed. Regarding the concordance of mRNA and protein expression, Pgp and Bcrp mRNA samples allow good estimations about the corresponding protein expression (for Pgp limited to the mdr1a isoform), but for Mrp2, pronounced deviation could be observed. All transporters showed considerable intra- and interindividual variability, especially at the protein level, making it problematic to take transporter expressions of small sections exemplary for general assumptions on intestinal abundances.
Action Sounds Modulate Arm Reaching Movements

Our mental representations of our body are continuously updated through multisensory bodily feedback as we move and interact with our environment. Although it is often assumed that these internal models of body-representation are used to successfully act upon the environment, only a few studies have actually looked at how body-representation changes influence goal-directed actions, and none have looked at this in relation to body-representation changes induced by sound. The present work examines this question for the first time. Participants reached for a target object before and after adaptation periods during which the sounds produced by their hand tapping a surface were spatially manipulated to induce a representation of an elongated arm. After adaptation, participants’ reaching movements were performed in a way consistent with having a longer arm, in that their reaching velocities were reduced. These kinematic changes suggest auditory-driven recalibration of the somatosensory representation of the arm morphology. These results provide support to the hypothesis that one’s represented body size is used as a perceptual ruler to measure objects’ distances and to accordingly guide bodily actions.
Political lessons from the global HIV/AIDS response to inform a rapid noncommunicable disease response.

The United Nations high-level meeting on noncommunicable diseases (NCDs) in September 2011 was an important milestone in global health. Discussions were dominated by the relative prioritization of prevention versus treatment for NCDs [1]. Wealthy states are cautious about promising a long-term commitment to NCD care in developing nations because of the costs of interventions and uncertainty about what interventions should be prioritized to yield positive outcomes.
Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears

Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof and Chichagof islands (ABC islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction.
Roles of lignin biosynthesis and regulatory genes in plant development

Abstract Lignin is an important factor affecting agricultural traits, biofuel production, and the pulping industry. Most lignin biosynthesis genes and their regulatory genes are expressed mainly in the vascular bundles of stems and leaves, preferentially in tissues undergoing lignification. Other genes are poorly expressed during normal stages of development, but are strongly induced by abiotic or biotic stresses. Some are expressed in non‐lignifying tissues such as the shoot apical meristem. Alterations in lignin levels affect plant development. Suppression of lignin biosynthesis genes causes abnormal phenotypes such as collapsed xylem, bending stems, and growth retardation. The loss of expression by genes that function early in the lignin biosynthesis pathway results in more severe developmental phenotypes when compared with plants that have mutations in later genes. Defective lignin deposition is also associated with phenotypes of seed shattering or brittle culm. MYB and NAC transcriptional factors function as switches, and some homeobox proteins negatively control lignin biosynthesis genes. Ectopic deposition caused by overexpression of lignin biosynthesis genes or master switch genes induces curly leaf formation and dwarfism.
The Relationship between Dioxin Congeners in the Breast Milk of Vietnamese Women and Sister Chromatid Exchange

The aim of this study was to clarify the relationship between dioxin concentrations in breast milk and the sister chromatid exchange (SCE) frequency in women from herbicide-sprayed and non sprayed areas. Blood samples were taken from 21 women with high TCDD (tetrachlorodibenzo-p-dioxin) levels from sprayed areas, 23 women with moderate TCDD levels from sprayed areas, and 19 women from non sprayed areas to determine their SCE frequency. The SCE frequencies for the high and moderate TCDD groups from the sprayed area and for the non sprayed area group were 2.40, 2.19, and 1.48 per cell, respectively. Multiple regression analysis showed that the standardized β values for 1,2,3,6,7,8-hexaCDD (β = 0.60), 1,2,3,4,6,7,8-heptaCDD (β = 0.64), and octaCDD (β = 0.65) were higher than those for TCDD (β = 0.34) and 1,2,3,7,8-pentaCDD (β = 0.42). The adjusted R2 value for polyCDDs (R2 = 0.38) was higher than that for polyCDD toxic equivalents (TEQ (toxic equivalents); R2 = 0.23). This study therefore shows that levels of hexa-, hepta-, and octaCDD, which were previously regarded as being less toxic than TCDD, are closely related to SCE frequency and that the level of dioxin (pg/g lipid) is potentially more useful as an indicator than TEQ value for explaining SCE frequency.
Composites of Wood and Biodegradable Thermoplastics: A Review

ABSTRACT This paper is an overview of current understanding in the areas of composites made from biodegradable thermoplastics and wood fillers. The review finds that the composite properties depend on the type of wood filler, the choice of polymer matrix, the wood filler content, the compatibilization technique used and the processing parameters. The extent of interfacial adhesion and the filler morphology are identified as the underlying factors that control the composite properties. Future research needs are identified, including establishment of fundamental relationships between quantified interfacial adhesion and end-use properties and advanced modelling of biodegradation processes.
An Efficient Algorithm for Sequential Circuit Test Generation

This paper presents an efficient sequential circuit automatic test generation algorithm. The algorithm is based on PODEM and uses a nine-valued logic model. Among the novel features of the algorithm are use of Initial Timeframe Algorithm and correct implementation of a solution to the Previous State Information Problem. The Initial Timeframe Algorithm, one of the most important aspects of the test generator, determines the number of timeframes required to excite the fault for which a test is to be derived and the number of timeframes required to observe the excited fault. Correct determination of the number of timeframes in which the fault should be excited (activated) and observed saves the test generator from performing unnecessary search in the input space. Test generation is unidirectional, i.e., it is done strictly in forward time, and flip-flops in the initial timeframe are never assigned a state that needs to be justified later. The algorithm saves both the good and the faulty machine states after finding a test to aid in subsequent test generation. The Previous State Information Problem, which has often been ignored by existing test generators, is presented and discussed in the paper. Experimental results are presented to demonstrate the effectiveness of the algorithm. >
Renal vasoconstriction in cirrhosis

Sacerdoti et al. (1) demonstrated that duplex ultrasound examination allows the detection of abnormal renal vascular impedance in patients with cirrhosis and ascites. Other studies confirmed these results (2 ,3 ) and demonstrated that an increasing resistivity index (RI) of intrarenal arteries has a prognostic role in predicting future renal failure (3). Sacerdoti et al. claimed that “this increase was already present in the nonascitic phase of the disease,” supporting “the hypothesis of underfilling as the cause of renal arterial vasoconstriction” in cirrhosis of the liver. Diuretic therapy could further increase renal RI and pulsatility index (PI). We are puzzled about these conclusions. The statistically significant difference between nonascitic cirrhotic patients and the control group seems to depend mainly on the low value of RI in the latter: in fact, this value is lower than those reported in other studies, whereas the one found in cirrhotic patients is similar. It is particularly disturbing that none of their control subjects had an RI higher than 0.59, in the middle of the normal range (3). In seven patients, RI and PI increased during diuretic therapy, but the authors should have demonstrated no change without therapy during the same time, or a decrease after therapy withdrawal, to confirm the hypothesis that diuretics can increase renal RI and PI. Patients with ascites are usually not hernodynamically stable; they accumulate fluid continuously and show signs of impaired renal perfusion, even in absence of diuretic therapy. In our opinion the higher values of renal RI and PI in patients on diuretics simply mean that
Author's Personal Copy Coordinate and Subspace Optimization Methods for Linear Least Squares with Non-quadratic Regularization Author's Personal Copy

This work addresses the problem of regularized linear least squares (RLS) with non-quadratic separable regularization. Despite being frequently deployed in many applications, the RLS problem is often hard to solve using standard iterative methods. In a recent work [M. Elad, Why simple shrinkage is still relevant for redundant representations? IEEE Trans. Inform. Theory 52 (12) (2006) 5559–5569], a new iterative method called parallel coordinate descent (PCD) was devised. We provide herein a convergence analysis of the PCD algorithm, and also introduce a form of the regularization function, which permits analytical solution to the coordinate optimization. Several other recent works [I. Daubechies, M. Defrise, C. De-Mol, An iterative thresholding algorithm for linear inverse problems with a sparsity constraint, Comm. which considered the deblurring problem in a Bayesian methodology, also obtained element-wise optimization algorithms. We show that the last three methods are essentially equivalent, and the unified method is termed separable surrogate functionals (SSF). We also provide a convergence analysis for SSF. To further accelerate PCD and SSF, we merge them into a recently developed sequential subspace optimization technique (SESOP), with almost no additional complexity. A thorough numerical comparison of the denoising application is presented, using the basis pursuit denoising (BPDN) objective function, which leads all of the above algorithms to an iterated shrinkage format. Both with synthetic data and with real images, the advantage of the combined PCD-SESOP method is demonstrated.
Relaxation‐compensated CEST‐MRI at 7 T for mapping of creatine content and pH – preliminary application in human muscle tissue in vivo

The small biomolecule creatine is involved in energy metabolism. Mapping of the total creatine (mostly PCr and Cr) in vivo has been done with chemical shift imaging. Chemical exchange saturation transfer (CEST) allows an alternative detection of creatine via water MRI. Living tissue exhibits CEST effects from different small metabolites, including creatine, with four exchanging protons of its guanidinium group resonating about 2 ppm from the water peak and hence contributing to the amine proton CEST peak. The intermediate exchange rate (≈ 1000 Hz) of the guanidinium protons requires high RF saturation amplitude B1. However, strong B1 fields also label semi‐solid magnetization transfer (MT) effects originating from immobile protons with broad linewidths (~kHz) in the tissue. Recently, it was shown that endogenous CEST contrasts are strongly affected by the MT background as well as by T1 relaxation of the water protons. We show that this influence can be corrected in the acquired CEST data by an inverse metric that yields the apparent exchange‐dependent relaxation (AREX). AREX has some useful linearity features that enable preparation of both concentration, and – by using the AREX‐ratio of two RF irradiation amplitudes B1 – purely exchange‐rate‐weighted CEST contrasts. These two methods could be verified in phantom experiments with different concentration and pH values, but also varying water relaxation properties. Finally, results from a preliminary application to in vivo CEST imaging data of the human calf muscle before and after exercise are presented. The creatine concentration increases during exercise as expected and as confirmed by 31P NMR spectroscopic imaging. However, the estimated concentrations obtained by our method were higher than the literature values: cCr,rest¯=24.5±3.74mM to cCr,ex¯=38.32±13.05mM . The CEST‐based pH method shows a pH decrease during exercise, whereas a slight increase was observed by 31P NMR spectroscopy. Copyright © 2015 John Wiley & Sons, Ltd.
Complete supine percutaneous nephrolithotripsy comparison with the prone standard technique.

PURPOSE PCNL (percutaneous nephrolithotripsy) is usually performed in the prone position. The supine position has potential advantages comparing with the prone position. Our objective is comparison between the outcome of PCNL in the complete supine position and the standard prone position. MATERIAL AND METHODS A total of 80 patients who underwent PCNL from February 2008 to June 2008 evaluated in a prospective manner, were randomly divided into two groups: 40 patients underwent prone PCNL and 40 patients underwent complete supine PCNL. We performed complete supine PCNL with no rolled towel under the flank and no change in leg position. Results in both positions were compared regarding technical aspects, operative time, stone free rate, complications and hospital stay, and were analyzed using t-test and chi-square. We considered P < 0.05 as significant. RESULTS Regardless the position, the pelvicaliceal system could be successfully approached in all patients. Mean operative time in supine group was 74.7 +/- 25.1 min and less than prone group (106.87 +/- 17.5) with a significant statistical difference (P < 0.0001). Stone free rate was 80% and 77.5% in prone and supine position respectively. Mean hospital stay was similar in both groups. Bleeding requiring transfusion in two groups had not significant statistical difference. We had not colon injury. CONCLUSION PCNL in supine position is safe, effective and suitable for the patients. It offers the potential advantages of better urethral access, less patient handling, needing drape only once, ability to perform simultaneous PCNL and ureteroscopic procedures, better control of the airway during procedures, thus reducing over-all operative time compared to traditional prone position and performing PCNL while the surgeon is sitting. It may be considered for most patients requiring PCNL.