Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis B virus reactivation in breast cancer patients receiving cytotoxic chemotherapy: A prospective study

Breast cancer is a rapidly increasing problem in many developing countries, and cytotoxic chemotherapy is now an integral part of its management. In several developing countries, the carriage of hepatitis B virus (HBV) in cancer patients may be as high as 12%, and such patients are at risk of developing fatal HBV reactivation during chemotherapy. HBV reactivation is well recognized in patients with hematological malignancies, but limited data are available on patients with other, more common, cancers, such as breast cancer. Recent data have suggested that increased viral replication, an indication of HBV reactivation, may precede clinical hepatitis. In the absence of serial HBV DNA monitoring, HBV reactivation during chemotherapy may have been underestimated. In this prospective study, breast cancer patients who were hepatitis B surface antigen (HBsAg) seropositive were followed up during chemotherapy. The main objectives were to determine the incidence of HBV reactivation in breast cancer patients undergoing conventional chemotherapy; to investigate whether “serial HBV DNA monitoring” improves the accuracy of diagnosing HBV reactivation when compared with previous schema that only measured HBV DNA at the time of clinical hepatitis (“conventional monitoring”); and to assess the clinical consequences as a result of developing the condition. The secondary objective was to identify risk factors associated with this condition. Over an 18‐month period, 41 patients were studied. Ten developed HBV reactivation by conventional monitoring criteria, but with serial HBV DNA monitoring, seven additional patients were diagnosed when increased HBV DNA levels were detected before, but not concomitant with, clinical hepatitis. Thus, a total of 17 patients (41%) developed HBV reactivation. Premature termination of chemotherapy or delay in treatment schedules occurred in 71% of the patients who developed viral reactivation, as compared with 33% in those who did not develop the condition (P = 0.019). No risk factors associated with the development of HBV reactivation could be identified. Serial monitoring of HBV DNA, in addition to liver function, increases the sensitivity of diagnosing of HBV reactivation, and helps explain some cases that would otherwise be labeled as “cryptogenic hepatitis,” for which concomitant HBV DNA measured at the time of hepatitis was undetectable. The present study highlights the importance of monitoring HBsAg‐seropositive patients who are receiving chemotherapy for common solid tumors such as breast cancer. J. Med. Virol. 70:553–561, 2003. © 2003 Wiley‐Liss, Inc.
Human Apolipoprotein A-II Protects Against Diet-Induced Atherosclerosis in Transgenic Rabbits

Objective—Apolipoprotein (apo) A-II is the second major apo of high-density lipoproteins, yet its pathophysiological roles in the development of atherosclerosis remain unknown. We aimed to examine whether apo A-II plays any role in atherogenesis and, if so, to elucidate the mechanism involved. Methods and Results—We compared the susceptibility of human apo A-II transgenic (Tg) rabbits to cholesterol diet-induced atherosclerosis with non-Tg littermate rabbits. Tg rabbits developed significantly less aortic and coronary atherosclerosis than their non-Tg littermates, while total plasma cholesterol levels were similar. Atherosclerotic lesions of Tg rabbits were characterized by reduced macrophages and smooth muscle cells, and apo A-II immunoreactive proteins were frequently detected in the lesions. Tg rabbits exhibited low levels of plasma C-reactive protein and blood leukocytes compared with non-Tg rabbits, and high-density lipoproteins of Tg rabbit plasma exerted stronger cholesterol efflux activity and inhibitory effects on the inflammatory cytokine expression by macrophages in vitro than high-density lipoproteins isolated from non-Tg rabbits. In addition, &bgr;-very-low-density lipoproteins of Tg rabbits were less sensitive to copper-induced oxidation than &bgr;-very-low-density lipoproteins of non-Tg rabbits. Conclusion—These results suggest that enrichment of apo A-II in high-density lipoprotein particles has atheroprotective effects and apo A-II may become a target for the treatment of atherosclerosis.
Complete Genome Sequences of Nine Bacillus cereus Group Phages

ABSTRACT We report the sequences of nine novel Bacillus cereus group bacteriophages: DIGNKC, Juglone, Nemo, Nigalana, NotTheCreek, Phrodo, SageFayge, Vinny, and Zuko. These bacteriophages are double-stranded DNA-containing Myoviridae isolated from soil samples using B. thuringiensis subsp. kurstaki as the host bacterium.
Ontological Smoothing for Relation Extraction

There is increasing interest in relation extraction, methods that convert natural language text into structured knowledge. The most successful techniques use supervised machine learning to generate extractors from sentences which have been labeled with the arguments of the relations of interest. Unfortunately, these methods require hundreds or thousands of training examples, which are expensive and time-consuming to produce. This paper presents ontological smoothing, a semi-supervised technique that exploits knowledge of a background ontology in order to learn extractors for a set of minimally-labeled relations. Ontological smoothing has three phases. The first step generates a mapping between the target relations and the background ontology. The second step uses knowledge-based weak supervision to heuristically generate new training examples for the target relations. The third step learns an extractor from a combination of the original and newly generated examples. Experiments on 61 relations across two target domains with Freebase as the background ontology show ontological smoothing can dramatically improve precision and recall.
The Option Value of Consumer Bankruptcy . ∗

This paper aims to contribute to the growing literature on the causes of consumer bankruptcy. It presents the consumer bankruptcy decision as an irreversible choice that has an embedded real option value. This allows the use of a well known framework for the study of decision making under uncertainty. The principal empirical finding is that cross-sectional variances of economic factors, such as unemployment, are strong predictors of bankruptcy rates and are consistent with the implications of the real options model. This supports anecdotal evidence that individuals are facing increased economic uncertainty and that suggests that uninsurable economic shocks are poorly characterized by local information. Finally, the paper concludes that policy regarding changes in the bankruptcy rate may have been disproportionately focused on credit variables such as utilization rates and supply of credit rather than exposure to risk. JEL Classification Codes: D14, I30, K45
Anytime Learning and Adaptation of Structured Fuzzy Behaviors

We present an approach to support effective learning and adaptation of behaviors for autonomous agents with reinforcement learning algorithms. These methods can identify control systems that optimize a reinforcement program, which is, usually, a straightforward representation of the designer's goals. Reinforcement learning algorithms usually are too slow to be applied in real time on embodied agents, although they provide a suitable way to represent the desired behavior. We have tackled three aspects of this problem: the speed of the algorithm, the learning procedure, and the control system architecture. The learning algorithm we have developed includes features to speed up learning, such as niche-based learning, and a representation of the control modules in terms of fuzzy rules that reduces the search space and improves robustness to noisy data. Our learning procedure exploits methodologies such as learning from easy missions and transfer of policy from simpler environments to the more complex. The architecture of our control system is layered and modular, so that each module has a low complexity and can be learned in a short time. The composition of the actions proposed by the modules is either learned or predefined. Finally, we adopt an anytime learning approach to improve the quality of the control system on-line and to adapt it to dynamic environments. The experiments we present in this article concern learning to reach another moving agent in a real, dynamic environment that includes nontrivial situations such as that in which the moving target is faster than the agent and that in which the target is hidden by obstacles.
Breast cancer brain metastases: differences in survival depending on biological subtype, RPA RTOG prognostic class and systemic treatment after whole-brain radiotherapy (WBRT).

BACKGROUND Patients with breast cancer brain metastasis are a heterogeneous group in relation to tumor biology and outcome. MATERIALS AND METHODS The group of 222 breast cancer patients with brain metastasis was divided into three biological subgroups. The propensity of biological subtypes for metastases to the brain and survivals depending on biological subtype, recursive partitioning analysis of Radiation Therapy Oncology Group (RPA RTOG) prognostic class and the use of systemic treatment after whole-brain radiotherapy were assessed. RESULTS The rate of patients with triple-negative, human epidermal growth factor receptor 2 (HER2)-positive and luminal breast cancer with brain metastases was 28%, 53% and 19%, respectively. Median survival from brain metastases in triple-negative, HER2-positive and luminal subtype was 3.7, 9 and 15 months, respectively. Median survival from brain metastases in RPA RTOG prognostic class I, II and III was 15, 11 and 3 months, respectively. In the luminal and in the triple-negative subtype, systemic therapy prolonged survival from 3 to 14 months and from 3 to 4 months, respectively. In HER2-positive subtype, median survival without further treatment, after chemotherapy and after chemotherapy with targeted therapy were 3, 8 and 11 months, respectively. CONCLUSIONS HER2-positive and triple-negative breast cancers have special predilection for metastases to the brain. Survival from brain metastases depended on performance status and the use of systemic treatment.
SOX10 Expression in Malignant Melanoma, Carcinoma, and Normal Tissues

Sry-related HMg-Box gene 10 (SOX10) is a nuclear transcription factor that plays an important role in melanocytic cell differentiation. It has been shown to be a sensitive marker of melanoma including spindle and desmoplastic subtypes. We assessed its frequency of expression in melanoma, carcinoma, benign nevi, and non-neoplastic tissues with routine immunohistochemistry for SOX10. The 109 primary melanoma included 49 epithelioid, 19 spindle cell, 22 desmoplastic, and 19 mixed spindle cell/desmoplastic melanoma. All primary, except 8 desmoplastic melanoma, and 11 metastatic melanoma were strongly and diffusely nuclear SOX10-positive. Six desmoplastic melanoma had ⩽10% cells positive, and 2 were <50% positive, all of 3+ intensity. Eighteen of 149 (12%) breast carcinoma were SOX10-positive. All 24 ovarian, 23 endometrial, 26 lung, and 25 colon carcinoma were SOX10-negative. All 43 benign nevi, 18 dysplastic nevi, 68 non-neoplastic and benign skins, and all 56 non-neoplastic breast tissue were SOX10-positive. The sensitivity and specificity for SOX10 in the diagnosis of melanoma are 1.0 and 0.93, respectively; the positive and negative predictive values are 0.87 and 1.0, respectively. SOX10 is a sensitive, specific marker for melanoma. As benign nevi also express SOX10, it cannot be used to differentiate between benign and malignant pigmented skin lesions. Only a small number of breast carcinoma (12%), and breast lobules, express SOX10; no carcinoma of the ovary, endometrium, lung, or colon expressed SOX10.
Transaction Specific Virtual Channel Allocation in QoS Supported On-chip Communication

We propose a scheme to reduce the number of virtual channel buffers used to implement logical channels multiplexed across the physical channel in a router output port for QoS supported on-chip communication. The number of virtual channels is minimized during the mapping of tasks to the NoC during the design time of a System on Chip (SoC) and a swarm intelligence-based Ant Colony Optimization (ACO) algorithm is used. We achieve on average 88% reduction in the number of virtual channels compared to a fixed allocation for the E3S embedded application benchmark suit and a collection of existing real-time embedded applications.
A dynamic adaptive self-organising hybrid model for text clustering

Clustering by document concepts is a powerful way of retrieving information from a large number of documents. This task in general does not make any assumption on the data distribution. For this task we propose a new competitive self-organising (SOM) model, namely the dynamic adaptive self-organising hybrid model (DASH). The features of DASH are a dynamic structure, hierarchical clustering, nonstationary data learning and parameter self-adjustment. All features are data-oriented: DASH adjusts its behaviour not only by modifying its parameters but also by an adaptive structure. The hierarchical growing architecture is a useful facility for such a competitive neural model which is designed for text clustering. We have presented a new type of self-organising dynamic growing neural network which can deal with the nonuniform data distribution and the nonstationary data sets and represent the inner data structure by a hierarchical view.
A Formal Framework for Automated Round-Trip Software Engineering in Static Aspect Weaving and Transformations

We present a formal framework for a recently introduced approach to automated round-trip software engineering (ARE) in source-level aspect weaving systems. Along with the formalization we improve the original method and suggest a new concept of weaving transactions in aspect-oriented programming (AOP). As the major contribution we formally show how, given a tree-shaped intermediate representation of a program and an ancillary transposition tree, manual edits in statically woven code can consistently be mapped back to their proper source of origin, which is either in the application core or in an element in the aspect space. The presented formalism is constructive. It frames AOP by generalizing static aspect weaving to classical tree transformations.
A tutorial on control-oriented modeling and control of wind farms

Wind turbines are often sited together in wind farms as it is economically advantageous. However, the wake inevitably created by every turbine will lead to a time-varying interaction between the individual turbines. Common practice in industry has been to control turbines individually and ignore this interaction while optimizing the power and loads of the individual turbines. However, turbines that are in a wake experience reduced wind speed and increased turbulence, leading to a reduced energy extraction and increased dynamic mechanical loads on the turbine, respectively. Neglecting the dynamic interaction between turbines in control will therefore lead to suboptimal behaviour of the total wind farm. Therefore, wind farm control has been receiving an increasing amount of attention over the past years, with the focus on increasing the total power production and reducing the dynamic loading on the turbines. In this paper, wind farm control-oriented modeling and control concepts are explained. In addition, recent developments and literature are discussed and categorized. This paper can serve as a source of background information and provides many references regarding control-oriented modeling and control of wind farms.
Analysis of lipid-composition changes in plasma membrane microdomains[S]

Sphingolipids accumulate in plasma membrane microdomain sites, such as caveolae or lipid rafts. Such microdomains are considered to be important nexuses for signal transduction, although changes in the microdomain lipid components brought about by signaling are poorly understood. Here, we applied a cationic colloidal silica bead method to analyze plasma membrane lipids from monolayer cells cultured in a 10 cm dish. The detergent-resistant fraction from the silica bead-coated membrane was analyzed by LC-MS/MS to evaluate the microdomain lipids. This method revealed that glycosphingolipids composed the microdomains as a substitute for sphingomyelin (SM) in mouse embryonic fibroblasts (tMEFs) from an SM synthase 1/2 double KO (DKO) mouse. The rate of formation of the detergent-resistant region was unchanged compared with that of WT-tMEFs. C2-ceramide (Cer) stimulation caused greater elevations in diacylglycerol and phosphatidic acid levels than in Cer levels within the microdomains of WT-tMEFs. We also found that lipid changes in the microdomains of SM-deficient DKO-tMEFs caused by serum stimulation occurred in the same manner as that of WT-tMEFs. This practical method for analyzing membrane lipids will facilitate future comprehensive analyses of membrane microdomain-associated responses.
Transmural Vaginal-to-Bladder Injury From an Obstructed Labor Pattern

BACKGROUND: A vesicovaginal fistula, among other devastating sequelae, is a complication that can arise from obstetric trauma such as prolonged obstructed labor patterns. These are rarely seen as obstetric-related complications in well-developed countries. They are thought to arise from direct ischemic injury that can occur between the fetal head and the adjacent tissues. CASE: A patient presented to the emergency room in obstructed labor. Examination revealed a crowning fetal head, no fetal heart tones, and purulent vaginal discharge. Postpartum, the patient experienced irritative voiding symptoms, vaginal stenosis, and cystoscopic evidence of injury to the bladder base. CONCLUSION: These findings may provide evidence of the transmural vaginal-to-bladder damage that can occur from obstructed labor.
Eeciently Updating Materialized Views

Query processing can be sped up by keeping frequently accessed users' views materialized. However , the need to access base relations in response to queries can be avoided only if the materialized view is adequately maintained. We propose a method in which all database updates to base relations are rst ltered to remove from consideration those that cannot possibly aaect the view. The conditions given for the detection of updates of this type, called irrelevant updates, are necessary and suucient and are independent of the database state. For the remaining database updates, a diierential algorithm can be applied to re-evaluate the view expression. The algorithm proposed exploits the knowledge provided by both the view deenition expression and the database update operations.
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression

MicroRNAs (miRNAs) are small (19–24 nt), nonprotein-coding nucleic acids that regulate specific ‘target’ gene products via hybridization to mRNA transcripts, resulting in translational blockade or transcript degradation. Although miRNAs have been implicated in numerous developmental and adult diseases, their specific impact on biological pathways and cellular phenotypes, in addition to miRNA gene promoter regulation, remain largely unknown. To improve and facilitate research of miRNA functions and regulation, we have developed MMIA (microRNA and mRNA integrated analysis), a versatile and user-friendly web server. By incorporating three commonly used and accurate miRNA prediction algorithms, TargetScan, PITA and PicTar, MMIA integrates miRNA and mRNA expression data with predicted miRNA target information for analyzing miRNA-associated phenotypes and biological functions by gene set analysis, in addition to analysis of miRNA primary transcript gene promoters. To assign biological relevance to the integrated miRNA/mRNA profiles, MMIA uses exhaustive human genome coverage, including classification into various disease-associated genes as well as conventional canonical pathways and Gene Ontology. In summary, this novel web server (cancer.informatics.indiana.edu/mmia) will provide life science researchers with a valuable tool for the study of the biological (and pathological) causes and effects of the expression of this class of interesting protein regulators.
Magnetoencephalography of frontotemporal dementia: spatiotemporally localized changes during semantic decisions

Behavioural variant frontotemporal dementia is a neurodegenerative disorder with dysfunction and atrophy of the frontal lobes leading to changes in personality, behaviour, empathy, social conduct and insight, with relative preservation of language and memory. As novel treatments begin to emerge, biomarkers of frontotemporal dementia will become increasingly important, including functionally relevant neuroimaging indices of the neurophysiological basis of cognition. We used magnetoencephalography to examine behavioural variant frontotemporal dementia using a semantic decision task that elicits both frontal and temporal activity in healthy people. Twelve patients with behavioural variant frontotemporal dementia (age 50–75) and 16 matched controls made categorical semantic judgements about 400 pictures during continuous magnetoencephalography. Distributed source analysis was used to compare patients and controls. The patients had normal early responses to picture confrontation, indicating intact visual processing. However, a predominantly posterior set of regions including temporoparietal cortex showed reduced source activity 250–310 ms after stimulus onset, in proportion to behavioural measures of semantic association. In contrast, a left frontoparietal network showed reduced source activity at 550–650 ms, proportional to patients’ deficits in attention and orientation. This late deficit probably reflects impairment in the neural substrate of goal-oriented decision making. The results demonstrate behaviourally relevant neural correlates of semantic processing and decision making in behavioural variant frontotemporal dementia, and show for the first time that magnetoencephalography can be used to study cognitive systems in the context of frontotemporal dementia.
No Teacher Left Behind: Subject Leadership that Promotes Teacher Leadership

This article presents some of the findings derived from a two-year qualitative study compromised of 51 semi-structured interviews with principals, subject leaders and classroom teachers belonging to three private K-12 schools in Beirut, Lebanon. In the context of investigating teacher leadership, this study highlights the aspects of the role of subject leaders in establishing and nourishing teacher leadership in their departments, particularly, three salutary research findings that portray how subject leaders impede or support such establishment are identified and explained. These are: (1) creating sub-cultures of professional collaboration and distributed leadership; (2) establishing bartered leadership structures; and (3) walking the talk of a shared system of teacher monitoring and evaluation.