Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine Needle Aspiration Cytology of Metastasis to Common and Unusual Sites

Fine needle aspiration cytology is highly accurate in the diagnosis of metastatic disease. In addition to establishing a diagnosis of metastatic malignancy, pathologists are increasingly asked to determine a possible primary site. Although a previous history of malignancy and characteristic cytomorphologic and immunocytochemical features are helpful in characterizing certain tumors, many metastatic malignancies lack a specific cytologic or immunocytochemical profile. This task can also be especially challenging if there is no history of malignancy, previous pathology is not available for review, or there is an unpredictable pattern of metastasis, potentially leading to a misdiagnosis of metastasis as a primary neoplasm. This article reviews the patterns of metastasis involving common (lymph nodes, bone, lung, liver, adrenal glands, salivary glands) and unusual (breast, thyroid, pancreas, kidney, small bones, eye, spleen) sites and the most likely primaries to spread to these organs. Familiarity with the variable patterns of metastasis in conjunction with cytologic features and selected ancillary studies will facilitate an accurate diagnosis.
Comparison of Restriction Fragment Length Polymorphism with the Polymorphic Guanine-Cytosine-Rich Sequence and Spoligotyping for Differentiation of Mycobacterium tuberculosis Isolates with Five or Fewer Copies of IS6110

ABSTRACT The use of IS6110 as a marker for molecular epidemiological studies is limited when a Mycobacterium tuberculosis isolate has five or fewer copies of IS6110. Restriction fragment length polymorphism analysis with a highly polymorphic GC-rich repetitive sequence located in the plasmid pTBN12 (PGRS RFLP) and spoligotyping (based on the polymorphism of the DR region) are two frequently used secondary typing methods. The aim of this study was to compare the performance of these two methods in a population-based study in San Francisco. We included all patients with culture-positive tuberculosis from 1999 to 2007 with IS6110 RFLP results presenting five or fewer bands. PGRS RFLP and spoligotyping were performed using standardized methods. We determined the concordance between the two methods regarding cluster status and the risk factors for an isolate to be in a cluster with each of the methods. Our data indicate that both methods had similar discriminatory power and that the risk factors associated with clustering by either method were the same. Although the cluster/unique status was concordant in 84% of the isolates, patients were clustered differently depending on the method. Therefore, the methods are not interchangeable, and the same method should be used for longitudinal studies.
Molecular Epidemiology of Genogroup II-Genotype 4 Noroviruses in the United States between 1994 and 2006

ABSTRACT Human noroviruses (NoVs) of genogroup II, genotype 4 (GII.4) are the most common strains detected in outbreaks of acute gastroenteritis worldwide. To gain insight into the epidemiology and genetic variation of GII.4 strains, we analyzed 773 NoV outbreaks reported to the CDC from 1994 to 2006. Of these NoV outbreaks, 629 (81.4%) were caused by GII viruses and 342 (44.2%) were caused by GII.4 strains. The proportion of GII.4 outbreaks increased from 5% in 1994 to 85% in 2006, but distinct annual differences were noted, including sharp increases in 1996, 2003, and 2006 each associated with newly emerging GII.4 strains. Sequence analysis of the full-length VP1 gene of GII.4 strains identified in this study and from GenBank segregated these viruses into at least 9 distinct subclusters which had 1.3 to 3.2% amino acid variation between strains in different subclusters. We propose that GII.4 subclusters be defined as having >5% sequence variation between strains. Our data confirm other studies on the rapid emergence and displacement of highly virulent GII.4 strains.
Characterization of a New Clinical Yeast Species, Candida tunisiensis sp. nov., Isolated from a Strain Collection from Tunisian Hospitals

ABSTRACT From a collection of yeast isolates isolated from patients in Tunisian hospitals between September 2006 and July 2010, the yeast strain JEY63 (CBS 12513), isolated from a 50-year-old male that suffered from oral thrush, could not be identified to the species level using conventional methods used in clinical laboratories. These methods include matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), germ tube formation, and the use of CHROMagar Candida and metabolic galleries. Sequence analysis of the nuclear rRNA (18S rRNA, 5.8S rRNA, and 26S rRNA) and internal transcribed spacer regions (ITS1 and ITS2) indicated that the ribosomal DNA sequences of this species were not yet reported. Multiple gene phylogenic analyses suggested that this isolate clustered at the base of the Dipodascaceae (Saccharomycetales, Saccharomycetes, and Ascomycota). JEY63 was named Candida tunisiensis sp. nov. according to several phenotypic criteria and its geographical origin. C. tunisiensis was able to grow at 42°C and does not form chlamydospores and hyphae but could grow as yeast and pseudohyphal forms. C. tunisiensis exhibited most probably a haploid genome with an estimated size of 10 Mb on at least three chromosomes. Using European Committee for Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) Candida albicans susceptibility breakpoints as a reference, C. tunisiensis was resistant to fluconazole (MIC = 8 μg/ml), voriconazole (MIC = 0.5 μg/ml), itraconazole (MIC = 16 μg/ml), and amphotericin B (MIC = 4 μg/ml) but still susceptible to posaconazole (MIC = 0.008 μg/ml) and caspofungin (MIC = 0.5 μg/ml). In conclusion, MALDI-TOF MS permitted the early selection of an unusual isolate, which was still unreported in molecular databases but could not be unambiguously classified based on phylogenetic approaches.
Explaining structured queries in natural language

Many applications offer a form-based environment for naïve users for accessing databases without being familiar with the database schema or a structured query language. User interactions are translated to structured queries and executed. However, as a user is unlikely to know the underlying semantic connections among the fields presented in a form, it is often useful to provide her with a textual explanation of the query. In this paper, we take a graph-based approach to the query translation problem. We represent various forms of structured queries as directed graphs and we annotate the graph edges with template labels using an extensible template mechanism. We present different graph traversal strategies for efficiently exploring these graphs and composing textual query descriptions. Finally, we present experimental results for the efficiency and effectiveness of the proposed methods.
Management of Acute and Chronic Nerve Injuries in the Multiple Ligament Injured Knee

Dislocation of the knee has long been recognized as a serious and potentially limb-threatening injury. Associated ligamentous injuries, fractures, and vascular and nerve injuries are common. Prompt recognition of a knee dislocation and appropriate treatment of associated injuries is necessary to minimize the complications of this severe and potentially devastating injury. Peroneal nerve injury occurs in approximately 28% of knee dislocations and cases of multiple ligament injury. Despite numerous advances in nerve repair techniques, the prognosis for nerve injuries after knee dislocation remains poor, with overall recovery of 40%. The authors review current recommendations for evaluation, treatment, and management of complications associated with nerve injury in knee dislocation, and suggest areas for future study to improve prognosis and treatment.
Probing Population Dynamics of Trypanosoma cruzi during Progression of the Chronic Phase in Chagasic Patients

ABSTRACT Our research aimed to characterize the genetic profiles of 102 Trypanosoma cruzi isolates recently obtained from 44 chronic chagasic patients from different regions of the states of Minas Gerais and Goiás in Brazil. At least two isolates were obtained from each patient at different times in order to study the parasite population dynamics during disease progression in the chronic phase. The isolates were characterized molecularly by genotyping the 3′ region of the 24Sα rRNA, the mitochondrial cytochrome oxidase subunit 2 (COII) gene, and the intergenic region of the spliced leader intergenic region (SL-IR) gene. Seventy-seven isolates were analyzed for nine microsatellite loci. The data presented here show a strong correlation between the T. cruzi lineage II (T. cruzi II) and human infection in these regions of Brazil. Interestingly, isolates from two patients were initially characterized (by rRNA genotyping) as T. cruzi I and hybrid strains, but subsequent analyses of the COII and SL-IR genes confirmed that those isolates belonged to T. cruzi III and a hybrid group, respectively. Our results confirm the risk of misclassifying T. cruzi isolates on the basis of analysis of a single molecular marker. The microsatellite profiles showed that different isolates obtained from the same patient were genetically identical and monoclonal. Exceptions were observed for T. cruzi isolates from two patients who presented differences for the SCLE11 locus and also from two other patients who showed amplification of three peaks for a microsatellite locus (TcAAAT6), implying that they were multiclonal. On the basis of the findings of the studies described here, we were not able to establish a correlation between the clinical forms of Chagas' disease and the genetic profiles of the T. cruzi isolates.
Twitter+: Build personalized newspaper for Twitter

Nowadays, microblogging services, e.g., Twitter, have played important roles in people's everyday lives. It enables users to publish and read text-based posts, known as “tweets” and interact with each other through re-tweeting or commenting. In the literature, many efforts have been devoted on exploiting the social property of Twitter. However, except the social component, Twitter itself has become an indispensable source for users to acquire useful information. To maximize its value, we expect to pay more attention on the media property of Twitter. To be good media, the first requirement is that it should provide an effective presentation of its news so that users are facilitated of reading. Currently, all tweets from followings are presented to the users and usually organized by their published timelines or coming sources. However, too few dimensions of presenting tweets hinder users from finding their interested information conveniently. In this demo, we presents “Twitter+”, which aims to enrich user's reading experiences in Twitter by providing multiple ways for them to explore tweets, such as keyword presentation, topic finding. It presents users an alternative interface to browse tweets more effectively.
Correlation of Bacterial Colonization Status between Mother and Child: the Generation R Study

ABSTRACT Determinants of bacterial colonization in children have been described. In the Generation R Study, a population-based cohort study, we determined whether the colonization statuses of mothers and children are correlated. Such a correlation was observed for Staphylococcus aureus and Haemophilus influenzae. Direct transmission, genetic susceptibility and/or unidentified environmental factors may play a role here.
Improved Detection of Respiratory Pathogens by Use of High-Quality Sputum with TaqMan Array Card Technology

ABSTRACT New diagnostic platforms often use nasopharyngeal or oropharyngeal (NP/OP) swabs for pathogen detection for patients hospitalized with community-acquired pneumonia (CAP). We applied multipathogen testing to high-quality sputum specimens to determine if more pathogens can be identified relative to NP/OP swabs. Children (<18 years old) and adults hospitalized with CAP were enrolled over 2.5 years through the Etiology of Pneumonia in the Community (EPIC) study. NP/OP specimens with matching high-quality sputum (defined as ≤10 epithelial cells/low-power field [lpf] and ≥25 white blood cells/lpf or a quality score [q-score] definition of 2+) were tested by TaqMan array card (TAC), a multipathogen real-time PCR detection platform. Among 236 patients with matched specimens, a higher proportion of sputum specimens had ≥1 pathogen detected compared with NP/OP specimens in children (93% versus 68%; P < 0.0001) and adults (88% versus 61%; P < 0.0001); for each pathogen targeted, crossing threshold (CT) values were earlier in sputum. Both bacterial (361 versus 294) and viral detections (245 versus 140) were more common in sputum versus NP/OP specimens, respectively, in both children and adults. When available, high-quality sputum may be useful for testing in hospitalized CAP patients.
YCSB+T: Benchmarking web-scale transactional databases

Database system benchmarks like TPC-C and TPC-E focus on emulating database applications to compare different DBMS implementations. These benchmarks use carefully constructed queries executed within the context of transactions to exercise specific RDBMS features, and measure the throughput achieved. Cloud services benchmark frameworks like YCSB, on the other hand, are designed for performance evaluation of distributed NoSQL key-value stores, early examples of which did not support transactions, and so the benchmarks use single operations that are not inside transactions. Recent implementations of web-scale distributed NoSQL systems like Spanner and Percolator, offer transaction features to cater to new web-scale applications. This has exposed a gap in standard benchmarks. We identify the issues that need to be addressed when evaluating transaction support in NoSQL databases. We describe YCSB+T, an extension of YCSB, that wraps database operations within transactions. In this framework, we include a validation stage to detect and quantify database anomalies resulting from any workload, and we gather metrics that measure transactional overhead. We have designed a specific workload called Closed Economy Workload (CEW), which can run within the YCSB+T framework. We share our experience with using CEW to evaluate some NoSQL systems.
Detection of Streptococcus pneumoniae Strain Cocolonization in the Nasopharynx

ABSTRACT Colonization with more than one distinct strain of the same species, also termed cocolonization, is a prerequisite for horizontal gene transfer between pneumococcal strains that may lead to change of the capsular serotype. Capsule switch has become an important issue since the introduction of conjugated pneumococcal polysaccharide vaccines. There is, however, a lack of techniques to detect multiple colonization by S. pneumoniae strains directly in nasopharyngeal samples. Two hundred eighty-seven nasopharyngeal swabs collected during the prevaccine era within a nationwide surveillance program were analyzed by a novel technique for the detection of cocolonization, based on PCR amplification of a noncoding region adjacent to the pneumolysin gene (plyNCR) and restriction fragment length polymorphism (RFLP) analysis. The numbers of strains and their relative abundance in cocolonized samples were determined by terminal RFLP. The pneumococcal carriage rate found by PCR was 51.6%, compared to 40.0% found by culture. Cocolonization was present in 9.5% (10/105) of samples, most (9/10) of which contained two strains in a ratio of between 1:1 and 17:1. Five of the 10 cocolonized samples showed combinations of vaccine types only (n = 2) or combinations of nonvaccine types only (n = 3). Carriers of multiple pneumococcal strains had received recent antibiotic treatment more often than those colonized with a single strain (33% versus 9%, P = 0.025). This new technique allows for the rapid and economical study of pneumococcal cocolonization in nasopharyngeal swabs. It will be valuable for the surveillance of S. pneumoniae epidemiology under vaccine selection pressure.
Swab Type, Moistening, and Preenrichment for Staphylococcus aureus on Environmental Surfaces

ABSTRACT We compared five swabs, dry or premoistened and with or without preenrichment, to detect surface contamination with Staphylococcus aureus. Sensitivities varied based on swab type, as follows: 71.9% and 75% for rayon, 71.2% for cotton, 81.3% for polyester, and 53.2% for calcium alginate. Preenrichment improved sensitivity (80%, versus 61.3% for direct-plated specimens), as did premoistening (83.4%, versus 57.5% for dry swabs). All of the premoistened, preenriched swabs were positive.
Body image and quality of life among men with prostate cancer

It is estimated that more than 218,000 men will be diagnosed with prostate cancer in the year 2007. With a mean age at diagnosis of 72, and extended long-term survival, prostate cancer represents a significant health problem among older men. Despite the fact that the treatment for prostate cancer has significant effects upon one’s physical appearance and functional ability, there exists a gap in the literature regarding body image in men with prostate cancer. Additionally, there is a large gap in our knowledge of the relationship of body image and QOL in men with prostate cancer. The purpose of this study was to describe changes in body image and quality of life among men with prostate cancer, to describe the relationship between the two, and to explore the differences in body image and quality of life related to treatment, age, duration of therapy and body mass index. The sample consisted of one hundred and thirty-two older men (> age 60) with prostate cancer, recruited from the oncology and urology out-patient departments at an urban Veterans Affairs Medical Center. The participants completed 2 established questionnaires, the Body Image Scale and the Quality of Life Index Cancer Version. Descriptive and inferential statistics were used in the analysis. For purposes of analysis, the sample was grouped according to treatment with ADT as part of therapy for prostate cancer. The ADT-naive group composed 34.1% of the sample (n = 45); the ADT group composed 65.9% of the sample (n = 87). Whether or not one received ADT was correlated with body image change: those men who received ADT had a greater perception of negative change. There was, however, no difference in
Pan London personalised budgets for rough sleepers

Purpose – The purpose of this paper is to positively confirm a new and different approach used to engage with entrenched rough sleepers, using the more personalised approach already adopted in social care. Design/methodology/approach – This is a first hand experience of the impact of the approach. Findings – That a personalised approach can achieve positive results with a hard to reach client group. Originality/value – This is the first published paper on this particular project.
A Case for Enhanced Linkage of Substance Abusers to Primary Medical Care

Alcohol and drug abuse continue to be problems of major significance throughout the United States. Although experts have advocated linking substance abusers with primary medical care to help achieve both individual and public health goals, few successful and generalizable methods for linkage have been developed. Specific potential benefits for such linkage include HIV testing and initiation of therapy, treatment of tuberculosis and sexually transmitted diseases, appropriate immunizations, cervical cancer screening, promotion of healthy behaviors regarding sexual and drug practices, and encouragement of cessation of substance use. Distributive or decentralized models linking patients receiving addiction treatment to existing primary medical care services need evaluation, as they may be more generalizable and cost-effective compared with on-site integrated programs. Health care providers and policy makers need to explore innovative approaches to bring substance abusers into a medical care system in a way that will provide continuity, comprehensiveness, and prevention so as to improve health care utilization patterns and reap benefits of improved addiction, behavioral, and health outcomes.
Tissue engineering in flexor tendon surgery: current state and future advances

Tissue engineering of flexor tendons addresses a challenge often faced by hand surgeons: the restoration of function and improvement of healing with a limited supply of donor tendons. Creating an engineered tendon construct is dependent upon understanding the normal healing mechanisms of the tendon and tendon sheath. The production of a tendon construct includes: creating a three-dimensional scaffold; seeding cells within the scaffold; encouraging cellular growth within the scaffold while maintaining a gliding surface; and finally ensuring mechanical strength. An effective construct incorporates these factors in its design, with the ultimate goal of creating tendon substitutes that are readily available to the reconstructive hand surgeon.
Sn-Cu nanocomposite anodes for rechargeable sodium-ion batteries.

Sn0.9Cu0. 1 nanoparticles were synthesized via a surfactant-assisted wet chemistry method, which were then investigated as an anode material for ambient temperature rechargeable sodium ion batteries. The Sn0.9Cu0. 1 nanoparticle-based electrodes exhibited a stable capacity of greater than 420 mA h g(-1) at 0.2 C rate, retaining 97% of their maximum observed capacity after 100 cycles of sodium insertion/deinsertion. Their performance is considerably superior to electrodes made with either Sn nanoparticles or Sn microparticles.
A Stewardship Approach To Optimize Antimicrobial Therapy through Use of a Rapid Microarray Assay on Blood Cultures Positive for Gram-Negative Bacteria

ABSTRACT A Gram-negative (GN) blood culture microarray assay with an antimicrobial stewardship program (ASP) intervention was evaluated in 126 patients with GN bacteremia. The median time to optimal therapy was shorter in the postintervention group than in the preintervention group (49.3 h versus 38.5 h, respectively; P = 0.0199). ASP can utilize microarray technology to decrease the time to optimal antimicrobial therapy.
A review of the classification of Dupuytren’s disease

Although much has been published about the treatment of Dupuytren’s disease, there is no clear consensus regarding the most effective form of treatment. Part of this uncertainty may result from the absence of a universal method of assessing this condition. We undertook a review of the literature in order to summarize the various methods by which Dupuytren’s disease has been measured and quantified. We included all articles that offered a classification or assessment system for the disease. We excluded articles that dealt solely with surgical technique (although inevitably there was some overlap). We conclude that there are many methods of assessment, but that none of them is perfect and that further work is needed in the field.