Miracle-dz/UniFAR-FTUs huggingface dataset:
Breast Cancer and Quality of Life: Medical Information Extraction from Health Forums

Internet health forums are a rich textual resource with content generated through free exchanges among patients and, in certain cases, health professionals. We tackle the problem of retrieving clinically relevant information from such forums, with relevant topics being defined from clinical auto-questionnaires. Texts in forums are largely unstructured and noisy, calling for adapted preprocessing and query methods. We minimize the number of false negatives in queries by using a synonym tool to achieve query expansion of initial topic keywords. To avoid false positives, we propose a new measure based on a statistical comparison of frequent co-occurrences in a large reference corpus (Web) to keep only relevant expansions. Our work is motivated by a study of breast cancer patients' health-related quality of life (QoL). We consider topics defined from a breast-cancer specific QoL-questionnaire. We quantify and structure occurrences in posts of a specialized French forum and outline important future developments.
Final report from the ASERNIP‐S audit of laparoscopic live‐donor nephrectomy

The Australian Safety and Efficacy Register of New Interventional Procedures − Surgical (ASERNIP‐S) audit of laparoscopic live‐donor nephrectomy commenced in 1999 and concluded in 2003. Six centres in Australia and New Zealand contributed data for 219 donor patients regarding perioperative and postoperative outcome of surgery and short‐term follow‐up. These data were compared with a recent systematic review of LLDN. The Australasian experience to date compared favourably with worldwide practice, both in terms of efficacy and safety for donors (at least in the short term). The collection of audit data, as this technique was introduced into the Australasian healthcare system, has allowed the local experience with this technique to be pooled and shared, resulting in the development of Australasian practice in line with world's best practice in this area.
The long noncoding RNA AK 139328 promotes the oncogenesis in thyroid cancer

Long noncoding RNAs (lncRNAs) play pivotal roles in various processes especially in oncogenesis. However, the function of lncRNA AK139328 in thyroid cancer development remains poorly understood. In current work, we have unraveled a novel function for AK139328 in thyroid cancer. We found that the expression of AK139328 was frequently increased in cancerous tissues and several cell lines. Meanwhile, upregulating AK139328 expression consistently promotes viability, invasion and cell cycle progression in TPC1 and 8505C cells contrary to the effect in groups with AK139328 knockdown. Higher AK139328 levels also correlate with poor overall and post progression survival. In addition, in vivo studies confirmed the oncogenic role of AK139328 as decreasing AK139328 level significantly attenuates Ki-67 staining and xenograft tumor growth. Mechanistic studies implied that upregulating AK139328 expression may promote epithelial-mesenchymal transition. Our study has identified a novel and oncogenic function of AK139328 in thyroid cancer and may provide potential insight into pharmaceutical intervention.
The Role of Spontaneous Variants in the Acquisition of Streptomycin Resistance by the Shigellae

Recent reports have clearly shown that bacteria tend to become rapidly resistant to streptomycin, both in vitro and clinically (Buggs, Bronstein, Hirshfeld, and Pilling, 1946; Miller and Bohnhoff, 1946; Youmans and Feldman, 1946). In the present work we will report on the development of streptomycin resistance in 12 strains of the shigellae and the nature of this in vitro resistance. A brief summary of this work has previously been reported (Klein and Kimmelman, 1946).
Identification of a Major Humoral Epitope in Slc30A8 (ZnT8)

The human zinc transporter Slc30A8 (ZnT8) is a major target of humoral autoimmunity in human type 1A diabetes. However, despite extensive conservation, the majority of human autoimmune sera fail to recognize the murine ortholog. Moreover, Slc30A8 appears not to be a significant target of humoral autoimmunity in the NOD mouse. We therefore “humanized” the murine protein by site‐directed mutagenesis. Only conversion of Q324 to arginine (equivalent to R325 in the human protein) partially restored reactivity to a pool of sera selected for high titers to the human probe. Additionally, the reciprocal mutation (human R325 to Q) abolished reactivity for 38/103 (36.9%) of ZnT8+ sera. We conclude that the C‐terminal domain of human ZnT8 contains at least two discrete epitopes, one of which is critically dependent upon the arginine residue at position 325.
The Relation between Customer and Time Averages in Queues

Brumelle has generalized the queueing formula L = λW to H = λG, where λ is the arrival rate and H and G are respectively time and customer averages of some queue statistics which have a certain relationship to each other but are otherwise arbitrary. Stidham has developed a simple proof of L = λW for each sample path, in which the only requirement is that λ and W be finite. In this note it is shown that Stidham's proof applies directly to the more general case of H = λG, provided λ and G are finite and a simple technical assumption is satisfied. The result is used to obtain time average probabilities in the queue GI/M/c/K. Finally, a counterexample is given to demonstrate that the technical assumption is not superfluous, even in the special case where H and G can be interpreted, respectively, as the time average number of units in the system and the average time spent by a unit in the system, as is the case with both L = λW and the application to the queue GI/M/c/K.
Statistical cells timing metrics characterization

To characterize statistical moments of cell delays and slopes, the standard method is Monte Carlo (MC) method. However, this method suffers from very high computational cost. In this paper, we propose a technique to quickly and accurately estimate Standard Deviation (SD) of standard cell delays and slopes. The proposed technique is based on the identification, performed with a reduced set of MC simulations, of delay and output slope SD functions that take input slope, output load and supply voltage as input arguments. These identified functions are then used to estimate SDs of delays and slopes at different operating conditions (input slope, output load, supply voltage). This proposed method provides at least 76% of CPU gains, with respect to MC, while keeping high accuracy.
Psychologic distress and maladaptive coping styles in patients with severe vs moderate asthma.

BACKGROUND Though several biologic factors have been suggested to play a role in the development and persistence of severe asthma, those associated with psychologic factors remain poorly understood. This study assessed levels of psychologic distress and a range of disease-relevant emotional and behavioral coping styles in patients with severe vs moderate asthma. METHODS Eighty-four patients (50% women, mean [M] age 46 years) with severe (n = 42) and moderate (n = 42) asthma were recruited. Severe asthma was defined according to American Thoracic Society criteria. Patients underwent demographic and medical history interviews and pulmonary function and allergy testing. Patients also completed questionnaires measuring asthma symptoms and the Millon Behavioral Medicine Diagnostic Inventory, which assesses psychologic distress and emotional/behavioral coping factors that influence disease progression and treatment. RESULTS After adjustment for covariates and applying a correction factor that reduced the significant P level to < . 01, patients with severe vs moderate asthma reported experiencing more psychologic distress, including worse cognitive dysfunction (F = 6.72, P < .01) and marginally worse anxiety-tension (F = 4.02, P < .05). They also reported worse emotional coping (higher illness apprehension [F = 9.57, P < .01], pain sensitivity [F = 10.65, P < .01], future pessimism [F= 8.53, P < .01], and interventional fragility [F = 7.18, P < .01]), and marginally worse behavioral coping (more functional deficits [F = 5.48, P < .05] and problematic compliance [F = 4.32, P < .05]). CONCLUSIONS Patients with severe asthma have more psychologic distress and difficulty coping with their disease, both emotionally and behaviorally, relative to patients with moderate asthma. Future treatment studies should focus on helping patients with severe asthma manage distress and cope more effectively with their illness, which may improve outcomes in these high-risk patients.
Occludin: One Protein, Many Forms

ABSTRACT Intercellular tight junctions (TJs) exhibit a complex molecular architecture involving the regulated cointeraction of cytoplasmic adaptor proteins (e.g., zonula occludens) and integral membrane linker proteins (e.g., occludin and claudins). They provide structural integrity to epithelial and endothelial tissues and create highly polarized barriers essential to homeostatic maintenance within vertebrate physiological systems, while their dysregulation is an established pathophysiological hallmark of many diseases (e.g., cancer, stroke, and inflammatory lung disease). The junctional complex itself is a highly dynamic signaling entity wherein participant proteins constantly undergo a blend of regulatory modifications in response to diverse physiological and pathological cues, ultimately diversifying the overall adhesive properties of the TJ. Occludin, a 65-kDa tetraspan integral membrane protein, contributes to TJ stabilization and optimal barrier function. This paper reviews our current knowledge of how tissue occludin is specifically modified at the posttranscriptional and posttranslational levels in diverse circumstances, with associated consequences for TJ dynamics and epithelial/endothelial homeostasis. Mechanistic concepts such as splice variance and alternate promoter usage, proteolysis, phosphorylation, dimerization, and ubiquitination are comprehensively examined, and possible avenues for future investigation highlighted.
Structural MRI volumetric analysis in patients with organic amnesia, 1: methods and comparative findings across diagnostic groups

BACKGROUND If they are to be replicable, MRI volume measurements require explicit definitions of structures and of criteria for delineating these structures on MRI. Previously published volumes in healthy subjects show considerable differences in measurements across different studies, including a fourfold variation in estimates of hippocampal volume. Previous neuroimaging reports in patients with Korsakoff syndrome have generally found widespread or non-specific change, whereas in patients with herpes encephalitis the extent of pathological involvement reported beyond the temporal lobes has varied. METHOD In the present study, a clear set of anatomical criteria and detailed MRI segmentation procedures were applied to measure whole brain, frontal and temporal lobe, and anterolateral and medial temporal volumes, as well as thalamic areas in patients with organic amnesia (from Korsakoff's syndrome, herpes encephalitis, and focal frontal lesions) as well as healthy controls. RESULTS Patients with Korsakoff's syndrome showed decreased thalamic measurements but no significant changes in the medial temporal lobes, whereas patients with herpes encephalitis showed severe medial temporal but not thalamic atrophy. In the patients with known frontal lobe lesions, quantitative analysis on MRI showed reduced frontal lobe volume but no significant temporal lobe or thalamic atrophy. CONCLUSION Quantified MRI can be a useful technique with which to examine brain-cognitive relations, provided that detailed techniques are explicitly described. In particular, specific patterns of volume change can be found in vivo in patients with Korsakoff's syndrome and those with herpes encephalitis.
Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation

RNA viruses have been used as model systems to understand the patterns and processes of molecular evolution because they have high mutation rates and are genetically diverse. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immune deficiency syndrome, is highly genetically diverse, and is classified into several groups and subtypes. However, it has been difficult to use its diverse sequences to establish the overall phylogenetic relationships of different strains or the trends in sequence conservation with the construction of phylogenetic trees. Our aims were to systematically characterize HIV-1 subtype evolution and to identify the regions responsible for HIV-1 subtype differentiation at the amino acid level in the Pol protein, which is often used to classify the HIV-1 subtypes. In this study, we systematically characterized the mutation sites in 2,052 Pol proteins from HIV-1 group M (144 subtype A; 1,528 subtype B; 380 subtype C), using sequence similarity networks. We also used spectral clustering to group the sequences based on the network graph structures. A stepwise analysis of the cluster hierarchies allowed us to estimate a possible evolutionary pathway for the Pol proteins. The subtype A sequences also clustered according to when and where the viruses were isolated, whereas both the subtype B and C sequences remained as single clusters. Because the Pol protein has several functional domains, we identified the regions that are discriminative by comparing the structures of the domain-based networks. Our results suggest that sequence changes in the RNase H domain and the reverse transcriptase (RT) connection domain are responsible for the subtype classification. By analyzing the different amino acid compositions at each site in both domain sequences, we found that a few specific amino acid residues (i.e., M357 in the RT connection domain and Q480, Y483, and L491 in the RNase H domain) represent the differences among the subtypes. These residues were located on the surface of the RT structure and in the vicinity of the amino acid sites responsible for RT enzymatic activity or function.
Integrating courseware with lessonware (computers in education)

An approach that integrates the advantages of structured courseware, whereby student monitoring provides feedback to students and teachers, with free interaction lessonware, which may raise student motivation and lends itself to exploratory and self-guided activities, is discussed. The efforts of the Centre for Educational Technology in this direction are described. <<ETX>>
Longitudinal study of trachomatous trichiasis in the Gambia

Aim: Investigation of the natural history of trachomatous trichiasis in the Gambia and of the outcome of self epilation and surgery for the condition. Methods: A 1 year longitudinal study of 190 subjects with trichiasis was performed. Major trichiasis cases (five lashes or more) were referred for surgery and minor trichiasis cases were advised to epilate. Outcome measures included progression of trichiasis and corneal scarring; attendance for and results of surgery. Results: 34 of 148 (23%, 95% CI 16 to 31) subjects with major trichiasis attended for surgery over the year. Progression from minor to major trichiasis occurred in 18 of 55 subjects (33%, 95% CI 21 to 47). Progression of corneal scarring occurred in 60 of 167 patients (36%, 95% CI 29 to 44). Clinically active trachoma and conjunctival bacterial isolation predicted progression of corneal opacity. Surgery was successful in 39 of 54 (72%) eyes. Conclusions: Despite the overall decline in trachoma in the Gambia, patients with both minor and major trichiasis remain at risk of developing corneal opacity. Active trachomatous inflammation and additional infection with bacteria may accelerate this process. Antibiotic treatment for trichiasis patients (in addition to surgery) should be investigated. Surgery for minor trichiasis may be indicated. Regular audit of surgical results is necessary with retraining where needed.
The Evolution of Management Information Systems: A Literature Review

The Management Information Systems MISs have been displaying considerable diversity during the evolution in the past decades. It comes such a big demand and challenge to draw an overarching picture of the evolutionary development of MISs. By systematically investigating the existing representative literature/research in MISs, especially by analyzing and modeling the MIS concepts, this paper first identifies the crises and challenges the traditional MIS has faced. Furthermore, by applying EBD, a design methodology, the author analyzes how these crises have been addressed, and as a result, how the classical MIS Pyramid is transformed and developed into an intelligence-integration framework for the understanding of MISs evolution, which is able to not only position various information systems, but also show how these systems are still interrelated in the whole process of the evolution. The two dimensional framework here for MISs is conceptual model based, and different from prior frameworks, is able to describe the overall evolution of management information systems dynamically, rather than just "partially", or "statically". This framework also provides a model applicable to the development of MISs and information technologies, thus it is has meanings not just academia but also practice. The descriptive validity or consolidation of the framework is demonstrated by applying it to published MISs' studies. Future trends and challenges of MISs are also discussed based on the framework in this paper.
Grasping novel objects

The work explained in this technical report is about evaluating some recent algorithms to grasp unforeseen objects for table clearance tasks. A tabletop object segmentation algorithm is proposed, and two recently published methods to generate grasps are discussed. The report presents practical considerations on how to use the segmentation algorithm and how to perform the tests with the evaluated algorithms for the generation of grasping poses. Finally, the results of both approaches and their comparison are discussed.
Bures volume of the set of mixed quantum states

We compute the volume of the (N2 − 1)-dimensional set N of density matrices of size N with respect to the Bures measure and show that it is equal to that of an (N2 − 1)-dimensional hyper-hemisphere of radius 1/2. For N = 2 we obtain the volume of the Uhlmann hemisphere, ½S3 ⊂ 4. We find also the area of the boundary of the set N and obtain analogous results for the smaller set of all real density matrices. An explicit formula for the Bures–Hall normalization constants is derived for an arbitrary N.
Why is HIV rarely transmitted by oral secretions? Saliva can disrupt orally shed, infected leukocytes.

BACKGROUND Oral transmission of human immunodeficiency virus (HIV) by the millions of HIV-infected individuals is a rare event, even when infected blood and exudate is present. Saliva of viremic individuals usually contains only noninfectious components of HIV indicating virus breakdown. OBJECTIVE To determine whether unknown HIV inhibitory mechanisms may explain the almost complete absence of infectious HIV in the saliva. METHODS Since most of the infectious HIV that is shed mucosally by asymptomatic individuals is found in, produced by, and transmitted by infected mononuclear leukocytes, we determined whether saliva, which is hypotonic, may disrupt these infected cells, thereby preventing virus multiplication and cell-to-cell transmission of HIV. Specifically, we measured (1) whether mononuclear leukocytes were lysed by saliva and (2) whether the lysis by saliva inhibits the multiplication of HIV and other viruses in infected leukocytes and other cells. RESULTS Saliva rapidly disrupted 90% or more of blood mononuclear leukocytes and other cultured cells. Concomitantly, there was a 10000-fold or higher inhibition of the multiplication of HIV and surrogate viruses. Further experiments indicated that the cell disruption is due to the hypotonicity of saliva: CONCLUSIONS Hypotonic disruption may be a major mechanism by which saliva kills infected mononuclear leukocytes and prevents their attachment to mucosal epithelial cells and production of infectious HIV, thereby preventing transmission. Implications for the known oral HIV transmission by milk and seminal fluid, as well as potential oral transmission to contacts and health care workers, are considered. This effective salivary defense may be applicable medically to interdict vaginal, rectal, and oral transmission of HIV by infected cells in seminal fluid or milk by the use of anticellular substances.
Feature-fusion based audio-visual speech recognition using lip geometry features in noisy enviroment

Humans are often able to compensate for noise degradation and uncertainty in speech information by augmenting the received audio with visual information. Such bimodal perception generates a rich combination of information that can be used in the recognition of speech. However, due to wide variability in the lip movement involved in articulation, not all speech can be substantially improved by audio-visual integration. This paper describes a feature-fusion audio-visual speech recognition (AVSR) system that extracts lip geometry from the mouth region using a combination of skin color filter, border following and convex hull, and classification using a Hidden Markov Model. The comparison of the new approach with conventional audio-only system is made when operating under simulated ambient noise conditions that affect the spoken phrases. The experimental results demonstrate that, in the presence of audio noise, the audio-visual approach significantly improves speech recognition accuracy compared with audio-only approach.
Predictive Analysis of Temporal and Overlapping Community Structures in Social Media

Digital media has some observable traces named communities. Several events such as split, merge, dissolve and survive happen to communities in social media. But what are significant features to predict these events? And to which extent a feature is relevant in a social media? To answer these questions, we perform a study on community evolution analysis and prediction. We employ three overlapping community detection (OCD) algorithms from literature to the case of time-evolving networks including social, email communication and co-authorship networks. Group evolution discovery (GED) technique is applied to track the identified communities. We compare structural properties of OCD algorithms and investigate most persistent communities over time. Furthermore, static and temporal features of a community are applied to build a logistic classifier for community evolution prediction (CEP). Results reveal important features to predict events happening to a community.