Miracle-dz/UniFAR-FTUs huggingface dataset:
Breast cancer classification and prognosis based on gene expression profiles from a population-based study

Comprehensive gene expression patterns generated from cDNA microarrays were correlated with detailed clinico-pathological characteristics and clinical outcome in an unselected group of 99 node-negative and node-positive breast cancer patients. Gene expression patterns were found to be strongly associated with estrogen receptor (ER) status and moderately associated with grade, but not associated with menopausal status, nodal status, or tumor size. Hierarchical cluster analysis segregated the tumors into two main groups based on their ER status, which correlated well with basal and luminal characteristics. Cox proportional hazards regression analysis identified 16 genes that were significantly associated with relapse-free survival at a stringent significance level of 0.001 to account for multiple comparisons. Of 231 genes previously reported by others [van't Veer, L. J., et al. (2002) Nature 415, 530-536] as being associated with survival, 93 probe elements overlapped with the set of 7,650 probe elements represented on the arrays used in this study. Hierarchical cluster analysis based on the set of 93 probe elements segregated our population into two distinct subgroups with different relapse-free survival (P < 0.03). The number of these 93 probe elements showing significant univariate association with relapse-free survival (P < 0.05) in the present study was 14, representing 11 unique genes. Genes involved in cell cycle, DNA replication, and chromosomal stability were consistently elevated in the various poor prognostic groups. In addition, glutathione S-transferase M3 emerged as an important survival marker in both studies. When taken together with other array studies, our results highlight the consistent biological and clinical associations with gene expression profiles.
Learning from Time-Changing Data with Adaptive Windowing

We present a new approach for dealing with distribution change and concept drift when learning from data sequences that may vary with time. We use sliding windows whose size, instead of being fixed a priori, is recomputed online according to the rate of change observed from the data in the window itself: The window will grow automatically when the data is stationary, for greater accuracy, and will shrink automatically when change is taking place, to discard stale data. This delivers the user or programmer from having to guess a time-scale for change. Contrary to many related works, we provide rigorous guarantees of performance, as bounds on the rates of false positives and false negatives. In fact, for some change structures, we can formally show that the algorithm automatically adjusts the window to a statistically optimal length. Using ideas from data stream algorithmics, we develop a time- and memory-ecient version of this algorithm, called ADWIN2. We show how to incorporate this strategy easily into
Advancing the preservation of cellular therapy products

Cell therapies are typically collected in one location, processed in a second location, and then administered in a third location. The ability to preserve the cells is critical to their clinical application. It improves patient access to therapies by increasing the genetic diversity of cells available. In addition, the ability to preserve cells improves the “manufacturability” of a cell therapy product by permitting the cells to be stored until the patient is ready for administration of the therapy, permitting inventory control of products, and improving management of staffing at cell therapy facilities. Finally, the ability to preserve cell therapies improves the safety of cell therapy products by extending the shelf life of a product and permitting completion of safety and quality control testing before release of the product for use. The support of the National Blood Foundation has been critical to our work on improving the quality of frozen and thawed cell therapy products through the development of a microfluidic device to remove dimethlysulfoxide (DMSO). We are also involved in research to replace DMSO with other agents that are less toxic to cells and patients. Finally, the need to advance the preservation of cell therapies was a driving force behind the development of the Biopreservation Core Resource (http://www.biocor.net), a national resource in biopreservation. New interest in translation of cell therapies from the bench to the patient's bedside has the potential to drive the transformation of preservation science, technology, and practice.
Serum Klotho (but not haplotypes) associate with the post-myocardial infarction status of older adults

OBJECTIVES: The number of deaths from vascular diseases is incredibly high worldwide, and reliable markers for major events are still needed. The current cross-sectional study investigated the association of Klotho haplotypes and Klotho serum levels with classic risk factors and a clinical history of vascular events. METHODS: Clinical, anthropometric, biochemical and nutritional assessments were conducted with 168 older adults, complemented by genotyping (rs9536314 and rs9527025) and the detection of serum Klotho (ELISA). RESULTS: Klotho levels and haplotypes did not associate with most classic risk factors for vascular events, including markers such as C-reactive protein and homocysteine. A positive association was only found between Klotho levels and the previous occurrence of a myocardial infarction by both correlational (p=0.006) and variance analyses (p<0.001), and these associations were independent of the context. CONCLUSION: Our results suggest that serum Klotho is higher in individuals with a clinical history of myocardial infarction but not with a history of coronary artery disease or stroke. None of the Klotho haplotypes were associated with the variables investigated herein.
Lysosome fusion to the cell membrane is mediated by the dysferlin C2A domain in coronary arterial endothelial cells

Dysferlin has recently been reported to participate in cell membrane repair in muscle and other cells through lysosome fusion. Given that lysosome fusion is a crucial mechanism that leads to membrane raft clustering, the present study attempted to determine whether dysferlin is involved in this process and its related signalling, and explores the mechanism underlying dysferlin-mediated lysosome fusion in bovine coronary arterial endothelial cells (CAECs). We found that dysferlin is clustered in membrane raft macrodomains after Fas Ligand (FasL) stimulation as detected by confocal microscopy and membrane fraction flotation. Small-interfering RNA targeted to dysferlin prevented membrane raft clustering. Furthermore, the translocation of acid sphingomyelinase (ASMase) to membrane raft clusters, whereby local ASMase activation and ceramide production – an important step that mediates membrane raft clustering – was attenuated. Functionally, silencing of the dysferlin gene reversed FasL-induced impairment of endothelium-dependent vasodilation in isolated small coronary arteries. By monitoring fluorescence quenching or dequenching, silencing of the dysferlin gene was found to almost completely block lysosome fusion to plasma membrane upon FasL stimulation. Further studies to block C2A binding and silencing of AHNAK (a dysferlin C2A domain binding partner), showed that the dysferlin C2A domain is required for FasL-induced lysosome fusion to the cell membrane, ASMase translocation and membrane raft clustering. We conclude that dysferlin determines lysosome fusion to the plasma membrane through its C2A domain and it is therefore implicated in membrane-raft-mediated signaling and regulation of endothelial function in coronary circulation.
Reduced coronary NO production in conscious dogs after the development of alloxan-induced diabetes.

The role of nitric oxide (NO) in the control of coronary blood flow (CBF) during the development of diabetes is unknown. To study this, mongrel dogs were chronically instrumented using sterile techniques for measurements of systemic hemodynamics and CBF. With heart rate controlled (150 beats/min), veratrine (1-10 μg/kg) caused dose-dependent increases in CBF; e.g., 5 μg/kg of veratrine increased CBF by 57 ± 7% from 41 ± 1.3 ml/min ( P < 0.05). The dogs developed diabetes 4-5 wk after injection of alloxan (40-60 mg/kg iv, blood glucose levels were 384 ± 18 mg/dl). After diabetes the same doses of veratrine caused smaller increases in CBF; i.e., 5 μg/kg of veratrine increased CBF by 32 ± 2% ( P < 0.05 compared with control) from 28 ± 4 ml/min. ACh- and adenosine-induced coronary vasodilation were reduced after diabetes as well. In anesthetized dogs after diabetes, vagal stimulation caused smaller increases in CBF. ACh and bradykinin caused smaller increases in[Formula: see text] production in coronary microvessels from diabetic dogs. Furthermore, despite the fact that mRNA for endothelial cell NO synthase from the aorta was increased twofold with the use of Northern blotting, the protein for aortic endothelial constitutive NO synthase was reduced by 66% after diabetes, as determined by Western blotting. Our results indicate that the NO-dependent coronary vasodilation by the Bezold-Jarisch reflex is impaired in conscious dogs after diabetes. The mechanism responsible for the impaired endothelium-dependent coronary vasodilation is most likely the decreased release of NO from the endothelium.
Psycho-social consequences of secondary infertility in Karachi.

OBJECTIVE To explore the experiences of social consequences among women suffering from secondary infertility. METHODS Descriptive case series of 400 women with secondary infertility attending tertiary care hospitals in Karachi, Pakistan. RESULTS More than two thirds (67.7%) of women stated that their inability to give live births or give birth to sons had resulted in marital dissonance. The respondents had been threatened for divorce (20%), husband's remarrying (38%) or to be returned to their parent's home (26%) by their in laws or husbands. Majority (68%) of the women threatened did not have any live births. However, those who had live births (32%) had a girl child only followed by difficulty in conceiving again. Secondary infertility was described as a cause of violence against infertile women. The women reported that they were being physically and verbally abused by husbands (10.5%) and in-laws (16.3%) for being infertile. Nearly 70% of women facing physical abuse and 60% of the women facing verbal abuse suffered severe mental stress. CONCLUSION The experience of infertility is a stressful condition itself. This becomes particularly traumatic with previous pregnancies ending up in abortions, stillbirths and neonatal/infant deaths or the live births being daughters only. However, it subjects the woman to contempt and exploitation resulting in severe psychological.
Using temporal IDF for efficient novelty detection in text streams

Novelty detection in text streams is a challenging task that emerges in quite a few different scenarios, ranging from email thread filtering to RSS news feed recommendation on a smartphone. An efficient novelty detection algorithm can save the user a great deal of time and resources when browsing through relevant yet usually previously-seen content. Most of the recent research on detection of novel documents in text streams has been building upon either geometric distances or distributional similarities, with the former typically performing better but being much slower due to the need of comparing an incoming document with all the previously-seen ones. In this paper, we propose a new approach to novelty detection in text streams. We describe a resource-aware mechanism that is able to handle massive text streams such as the ones present today thanks to the burst of social media and the emergence of the Web as the main source of information. We capitalize on the historical Inverse Document Frequency (IDF) that was known for capturing well term specificity and we show that it can be used successfully at the document level as a measure of document novelty. This enables us to avoid similarity comparisons with previous documents in the text stream, thus scaling better and leading to faster execution times. Moreover, as the collection of documents evolves over time, we use a temporal variant of IDF not only to maintain an efficient representation of what has already been seen but also to decay the document frequencies as the time goes by. We evaluate the performance of the proposed approach on a real-world news articles dataset created for this task. The results show that the proposed method outperforms all of the baselines while managing to operate efficiently in terms of time complexity and memory usage, which are of great importance in a mobile setting scenario.
Automatic classification of citation function

Citation function is defined as the author's reason for citing a given paper (e.g. acknowledgement of the use of the cited method). The automatic recognition of the rhetorical function of citations in scientific text has many applications, from improvement of impact factor calculations to text summarisation and more informative citation indexers. We show that our annotation scheme for citation function is reliable, and present a supervised machine learning framework to automatically classify citation function, using both shallow and linguistically-inspired features. We find, amongst other things, a strong relationship between citation function and sentiment classification.
Inputs to the Dorsal Striatum of the Mouse Reflect the Parallel Circuit Architecture of the Forebrain

The basal ganglia play a critical role in the regulation of voluntary action in vertebrates. Our understanding of the function of the basal ganglia relies heavily upon anatomical information, but continued progress will require an understanding of the specific functional roles played by diverse cell types and their connectivity. An increasing number of mouse lines allow extensive identification, characterization, and manipulation of specified cell types in the basal ganglia. Despite the promise of genetically modified mice for elucidating the functional roles of diverse cell types, there is relatively little anatomical data obtained directly in the mouse. Here we have characterized the retrograde labeling obtained from a series of tracer injections throughout the dorsal striatum of adult mice. We found systematic variations in input along both the medial–lateral and anterior–posterior neuraxes in close agreement with canonical features of basal ganglia anatomy in the rat. In addition to the canonical features we have provided experimental support for the importance of non-canonical inputs to the striatum from the raphe nuclei and the amygdala. To look for organization at a finer scale we have analyzed the correlation structure of labeling intensity across our entire dataset. Using this analysis we found substantial local heterogeneity within the large-scale order. From this analysis we conclude that individual striatal sites receive varied combinations of cortical and thalamic input from multiple functional areas, consistent with some earlier studies in the rat that have suggested the presence of a combinatorial map.
Optimizing Grammars for Minimum Dependency Length

We examine the problem of choosing word order for a set of dependency trees so as to minimize total dependency length. We present an algorithm for computing the optimal layout of a single tree as well as a numerical method for optimizing a grammar of orderings over a set of dependency types. A grammar generated by minimizing dependency length in unordered trees from the Penn Treebank is found to agree surprisingly well with English word order, suggesting that dependency length minimization has influenced the evolution of English.
Online Submission ID : 307 Stable

Visual quality, low computational cost, and numerical stability are foremost goals in computer animation. An important ingredient in achieving these goals is the conservation of fundamental motion invariants. For example, rigid and deformable body simulation benefits greatly from conservation of linear and angular momenta. In the case of fluids, however, none of the current techniques focuses on conserving invariants, and consequently, they often introduce a visually disturbing numerical diffusion of vorticity. Visually just as important is the resolution of complex simulation domains. Doing so with regular (even if adaptive) grid techniques can be computationally delicate. In this paper, we propose a novel technique for the simulation of fluid flows. It is designed to respect the defining differential properties, i.e., the conservation of circulation along arbitrary loops as they are transported by the flow. Consequently, our method offers several new and desirable properties: (1) arbitrary simplicial meshes (triangles in 2D, tetrahedra in 3D) can be used to define the fluid domain; (2) the computations are efficient due to discrete operators with small support; (3) the method is stable for arbitrarily large time steps; (4) it preserves discrete circulation avoiding numerical diffusion of vorticity; and (5) its implementation is straightforward.
Intermittent Cyclic Mechanical Tension-Induced Calcification and Downregulation of ankh Gene Expression of End Plate Chondrocytes

Study Design. Intermittent Cyclic Mechanical Tension (ICMT) was applied to end plate chondrocytes by using an FX-4000T Flexercell Tension Plus unit (Flexcell International Corporation, Hillsborough, NC). Changes of end plate chondrocytes were observed after ICMT stimulation. Objective. To investigate the relationship between mechanical stimulation and calcification of end plate chondrocytes. Summary of Background Data. Previous study showed that end plate calcification was related to mechanical stress, but there was no clear evidence to indicate whether or not mechanical stimulation could induce calcification of end plate chondrocytes in vitro. Methods. Rat end plate chondrocytes were cultured and ICMT (strain at 0.5 Hz sinusoidal curve at 10% elongation) was applied for 25 days, 4 hours a day and continued to culture for 5 days. End plate chondrocytes were incubated for 12 hours in the presence or absence of 10 ng/mL of transforming growth factor-&bgr;1 (TGF-&bgr;1) (prepared from a stock solution at 10 &mgr;g/mL in 2 mM citric acid containing 2 mg/mL bovine serum albumin) in MEM/F-12 containing a final concentration of 1% FCS. End plate chondrocytes calcification was stained by alizarin red S (AR-S). End plate chondrocytes viability was examined by LIVE/DEAD viability/cytotoxicity kit (Invitrogen, Carlsbad, CA). Related gene expression was examined by reverse transcription-polymerase chain reaction and Western blot. Results. LIVE/DEAD assay verified that the nonloading (NC) group and the ICMT group end plate chondrocytes remained adherent, with no change in viability after the application of ICMT. Alizarin red staining showed that ICMT induced the calcification of end plate chondrocytes. Real-time reverse transcription-polymerase chain reaction showed that mRNA expression of endogenous TGF-&bgr;1 decreased and mRNA expression of type I, type X, osteocalcin and osteopontin increased after ICMT. The ankh gene expression of both mRNA and protein levels decreased in the ICMT stimulation. The ankh gene expression of both mRNA and protein levels increased in TGF-&bgr;1 stimulation. Compared with NC group, the alkaline phosphatase activities significantly increased in ICMT group. Conclusion. Our results directly showed that ICMT induced the calcification and downregulation of ankh gene expression of end plate chondrocytes, which may be caused by the endogenous TGF-&bgr;1.
Exceptional prevalence of interatrial block in a general hospital population

Background: Interatrial block (IAB: P wave ≥ 110 ms) is a strong correlate of left atrial (LA) enlargement and an important predictor of supraventricular tachyarrhythmias, notably atrial fibrillation and flutter. It is surprising that, despite its association with arrhythmias and its effects on the electromechanical properties of the left atrium, there is widespread neglect of this common abnormality.
Antioxidant-Chemoprevention Diet Ameliorates Late Effects of Total-Body Irradiation and Supplements Radioprotection by MnSOD-Plasmid Liposome Administration

Abstract Many acute and chronic effects of ionizing radiation are mediated by reactive oxygen species and reactive nitrogen species, which deplete antioxidant stores, leading to cellular apoptosis, stem cell depletion and accelerated aging. C57BL/6NHsd mice receiving intravenous MnSOD-PL prior to 9.5 Gy total-body irradiation (TBI) show increased survival from the acute hematopoietic syndrome, and males demonstrated improved long-term survival (Epperly et al., Radiat. Res. 170, 437–444, 2008). We evaluated the effect of an antioxidant-chemopreventive diet compared to a regular diet on long-term survival in female mice. Twenty-four hours before the LD50/30 dose of 9.5 Gy TBI, subgroups of mice were injected intravenously with MnSOD-PL (100 μg plasmid DNA in 100 μl of liposomes). Mice on either diet treated with MnSOD-PL showed decreased death after irradiation compared to irradiated mice on the house diet alone (P = 0.031 for the house diet plus MnSOD-PL or 0.015 for antioxidant diet plus MnSOD-PL). The mice on the antioxidant-chemoprevention diet alone or with MnSOD-PL that survived 30 days after irradiation had a significant increase in survival compared to mice on the regular diet (P = 0.04 or 0.01, respectively). In addition, mice treated with MnSOD-PL only and surviving 30 days after radiation also had increased survival compared to those on the regular diet alone (P = 0.02). Survivors of acute ionizing radiation damage have ameliorated life shortening if they are fed an antioxidant-chemopreventive diet.
A Clinicopathological Survey of Basal Cell Carcinoma in an Iranian Population

Statement of Problem: Basal cell carcinoma (BCC), the most common skin cancer, is a locally invasive malignant epidermal tumor with ulceration and destruction of underlying structures. Purpose: The purpose of this study was clinicopathological evaluation of BCC in the state and the private pathology centers in Hamadan province during 1990-2010. Materials and Method: In this retrospective study all histopathologically proven cases of BCC were reviewed and the related information including age, gender, place of residency and number of tumors for the patients alongside with the site of occurrence, size, histopathological and clinical type of the lesions were collected and then statistically analyzed, using SPSS software. Results: A total of 804 incidents of BCC were diagnosed in 746 patients (296 females and 450 males) with the most affected site being in the head-face (84.8%), neck (2.6%), trunk (1.6%) and limbs (0.9 %) and 10.1% cases with unknown site. The mean age for the patients was 61.77±13.75 years (63.07± 13.44 for males, 59.81 ± 14.01 for females) and the highest frequency (27.2%) occurred among 60–69 years age group. Nodular type was the most common clinical and histopathological BCC lesions studied whereas the mean size of the lesions was 15.67 ± 11.06 mm with more frequency rate in urban than rural regions. Conclusion: This study focuses on the survey of BCC in Hamadan province but regarding to insufficiency of the data collected by state and provincial pathology centers about the BCC cases reported; it is highly recommended to apply comprehensive questionnaire, which are designated by skillful professionals who are familiar with the lesion nationally.