Miracle-dz/UniFAR-FTUs huggingface dataset:
Establishment and characterization of an EBNA-negative human lymphoma cell line (BHL-89).

BACKGROUND The aim of the work was to establish human malignant lymphomas in culture, in order to study the biological characteristics and drug sensitivity of lymphomas of human lymphoid origin. MATERIALS AND METHODS Lymph nodes of patients were explanted and kept in cultures using conventional tissue culture methods. Cytogenetic methods were used for karyotype analysis. Clonogenic assay was applied to test drug sensitivity. The tumorigenic capacity of the cells was determined by inoculating them into immunosuppressed mice. Immunological and other markers were examined with conventional techniques. RESULTS A cell line, BHL-89, was established in culture from a patient with B-cell type non-Hodgkin's malignant lymphoma. Cells started to grow after a few days without a feeder layer in stationary suspension. The population doubling time was 48 h. The cells were hyperploid, and non-random aberrations were +1, -15, +14q+. Cloning efficiency in soft agar was found to be as high as 50-60%. The cells expressed markers characteristic of early B cells. The BHL-89 cells were Epstein-Barr nuclear antigen (EBNA) negative. They produced tumors when 10(7) cells were injected into immunosuppressed mice. The cells were sensitive to dibromodulcitol (Elobromol), an alkylating antitumor drug, and resistant to the phorbol ester TPA. CONCLUSIONS The established EBNA-negative BHL-89 cell line has a few unique characteristics, e.g. rapid establishment without feeder cells, origin from the lymph node of an adult patient, high clonogenicity in soft agar, and resistance to TPA. The cell line is suitable for studying the nature of B lymphomas and testing compounds against lymphoproliferative disorders.
ANN-based adaptive motion and posture control of an inverted pendulum with unknown dynamics

In this paper, an artificial neural network (ANN) based control scheme is introduced for the inverted pendulum motion and posture control problem. The adaptive control strategy consists of a Lyapunov stability-based online weights adaptation that provides asymptotic tracking while learning the nonlinear inverted pendulum system's dynamics. Unlike other control strategies, no a priori offline training, weights initialization, or parameters knowledge is required. Experiments for different situations highlight the performance of the proposed controller in compensating for friction nonlinearities, in the form of Coulomb friction. Furthermore, the neural networks inherent parallelism makes them a good candidate for implementation in real-time electromechanical systems.
Time-Domain Analysis of Building Shielding Against Lightning Electromagnetic Fields

The shielding performance of different buildings in presence of indirect lightning return strokes are investigated directly in the time domain. To this end, a sensitivity analysis is conducted by varying the channel geometrical characteristics and considering three different buildings. The performance is evaluated by adopting the time-domain shielding parameters recently proposed, which appear to be suitable for shielding studies in presence of lightning electromagnetic pulses. The results confirm the usefulness of introducing different parameters to fully characterize the shielding behavior of buildings exposed to lightning electromagnetic fields.
Initial Rotor Position Estimation Using Zero-Sequence Carrier Voltage for Permanent-Magnet Synchronous Machines

Both rotating and anticlockwise pulsating signal injection methods based on zero-sequence voltage sensing have been reported to have large signal-to-noise ratio and bandwidths, and great stability for the sensorless control of permanent-magnet synchronous machines. However, the initial rotor position estimation and magnetic polarity identification using zero-sequence voltage have not been investigated. Therefore, this paper presents two types of magnetic polarity identification methods, based on the amplitude variation of zero-sequence voltage due to saturation changing, and based on the secondary harmonics of zero-sequence voltage, for the two carrier injection methods, respectively. It is found that the amplitude variation based method using zero-sequence voltage has higher detection sensitivity for the real magnetic polarity compared to the conventional method using the carrier current. In contrast, the secondary harmonic based identification method using zero-sequence voltage for rotating signal injection has the advantage of fast response, and moreover has large signal amplitude and less distortion compared to the conventional secondary carrier current harmonics. However, the secondary harmonic method loses the capability for polarity detection for the anticlockwise pulsating injection method. Experiments are carried out on a laboratory permanent-magnet machine to verify the theoretical analyses.
FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations

In order to identify somatic focal copy number aberrations (CNAs) in cancer specimens and to distinguish them from germ-line copy number variations (CNVs), we developed the software package FocalCall. FocalCall enables user-defined size cutoffs to recognize focal aberrations and builds on established array comparative genomic hybridization segmentation and calling algorithms. To distinguish CNAs from CNVs, the algorithm uses matched patient normal signals as references or, if this is not available, a list with known CNVs in a population. Furthermore, FocalCall differentiates between homozygous and heterozygous deletions as well as between gains and amplifications and is applicable to high-resolution array and sequencing data. AVAILABILITY AND IMPLEMENTATION: FocalCall is available as an R-package from: https://github.com/OscarKrijgsman/focalCall. The R-package will be available in Bioconductor.org as of release 3.0.
Purification, Reconstitution, and Inhibition of Cytochrome P-450 Sterol Δ22-Desaturase from the Pathogenic Fungus Candida glabrata

ABSTRACT Sterol Δ22-desaturase has been purified from a strain of Candida glabrata with a disruption in the gene encoding sterol 14α-demethylase (cytochrome P-45051; CYP51). The purified cytochrome P-450 exhibited sterol Δ22-desaturase activity in a reconstituted system with NADPH–cytochrome P-450 reductase in dilaurylphosphatidylcholine, with the enzyme kinetic studies revealing a Km for ergosta-5,7-dienol of 12.5 μM and aVmax of 0.59 nmol of this substrate metabolized/min/nmol of P-450. This enzyme is encoded by CYP61 (ERG5) in Saccharomyces cerevisiae, and homologues have been shown in the Candida albicans andSchizosaccharomyces pombe genome projects. Ketoconazole, itraconazole, and fluconazole formed low-spin complexes with the ferric cytochrome and exhibited type II spectra, which are indicative of an interaction between the azole moiety and the cytochrome heme. The azole antifungal compounds inhibited reconstituted sterol Δ22-desaturase activity by binding to the cytochrome with a one-to-one stoichiometry, with total inhibition of enzyme activity occurring when equimolar amounts of azole and cytochrome P-450 were added. These results reveal the potential for sterol Δ22-desaturase to be an antifungal target and to contribute to the binding of drugs within the fungal cell.
Cognitive Approach to the Assessment of Limb Apraxia

A new instrument for the assessment of the different levels of gesture processing, as identified by recent cognitive models of apraxia, is presented. The battery comprises thirteen tasks—eight assess the production of meaningful gestures both on command and on imitation, four tasks assess the ability to recognize and identify gestures, and one task assesses imitation of meaningless gestures. The battery encompasses a novel test of gesture production on visual command. A total of 60 healthy British volunteers were tested with the entire battery. On the whole, participants made more errors with pantomimes than with other tasks. Their scores served as norms.
SNAI 2 modulates colorectal cancer 5-fluorouracil sensitivity through miR 145 repression

Epithelial-to-mesenchymal transition (EMT) has been associated with poor treatment outcomes in various malignancies and is inversely associated with miRNA-145 expression. Therefore, we hypothesized that SNAI2 (Slug) may mediate 5FU chemotherapy resistance through inhibition of miR-145 in colorectal cancer (CRC) and thus, represents a novel therapeutic target to enhance current CRC treatment strategies. Compared to parental DLD1 colon cancer cells, 5FU-resistant (5FUr) DLD1 cells demonstrated features of EMT, including >2-fold enhanced invasion (p<0.001) and migration, suppressed E-Cadherin expression, and 2fold increased SNAI2 expression. DLD1 and HCT116 cells with stable expression of SNAI2 (DLD1/SNAI2; HCT116/SNAI2) also demonstrated EMT features such as the decreased ECadherin, as well as significantly decreased miR-145 expression, as compared to control empty vector cells. Based on a miR-145 luciferase promoter assay, we demonstrated that SNAI2 repressed activity of the miR-145 promoter in the DLD1 and HCT116 cells. In addition, the ectopic expressing SNAI2 cell lines demonstrated decreased 5FU sensitivity and conversely, miR-145 replacement significantly enhanced 5FU sensitivity. In the parental SW620 colon cancer cell line with high SNAI2 and low miR-145 levels, inhibition of SNAI2 directly with short hairpin sequence for SNAI2 and miR-145 replacement therapy both decreased Vimentin expression and increased in vitro 5FU sensitivity. In pre-treatment rectal cancer patient biopsy samples, low miR-145 expression levels correlated with poor response to neoadjuvant 5FU based chemoradiation. These results suggested that the SNAI2:miR-145 pathway may represent a novel clinical therapeutic target in CRC and may serve as a response predictor to chemoradiation therapy. on June 20, 2017. © 2014 American Association for Cancer Research. mct.aacrjournals. org Downloaded from Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Author Manuscript Published OnlineFirst on September 23, 2014; DOI: 10.1158/1535-7163.MCT-14-0207
Genetic diversity and population structure of Colletia paradoxa (Rhamnaceae) a medicinal species threatened with extinction in Brazil

Abstract In order to obtain a better knowledge about the endangered species Colletia paradoxa (Rhamnaceae), which appears in fragmented populations, a study was carried out with six populations from different physiographic regions of Rio Grande do Sul and Santa Catarina states, Brazil. The objective of this study is to investigate the real conditions of genetic diversity in populations, through the use of inter simple sequence repeat (ISSR) molecular marker, and to evaluate the distribution of genetic diversity among and within populations, in order to plan conservation and management strategies. Five selected primers produced 112 DNA fragments in 46 samples from individuals that were evaluated. The result of the analyses showed 100% polymorphism. Nei’s genetic diversity index (H) was 0.3083. Shannon’s information index (I) was 0.4880. Bayesian inference of clustering performed by Structure revealed the most likely K = 4 to C. paradoxa. The analysis of molecular variance among all populations showed that the greatest genetic diversity occurs within the populations (82%), while among them there is less differentiation (18%), although in some populations good levels of genetic migration occur (Nm = 1.0465) indicating that genetic exchanges among populations of C. paradoxa are still occurring.
Proteomic analysis of amniotic fluid in pregnancies with Down syndrome

Proteomic analysis is widely used for the detection of diagnostic markers. In the present study amniotic fluid supernatants (AFS) from pregnancies with Down syndrome (DS) fetuses and from chromosomally normal fetuses in the 17th week of gestation were analyzed by 2‐DE. Gel comparison revealed significant differences in the two groups. Spots with different expression levels were excised and proteins were identified by MALDI‐MS and nano‐ESI‐MS/MS. Splicing factor arginine/serine‐rich 4 (SFRS4; Q08170) was present only in AFS from DS fetuses and completely absent in the control group. Quantitative differences were detected for alpha‐1‐microglobulin (AMBP; P02760), collagen alpha 1 (I) chain (CO1A1; P02452), collagen alpha 1 (III) chain (CO3A1; P02461), collagen alpha 1 (V) chain d (CO5A1; P20908), and basement membrane‐specific heparin sulfate proteoglycan core protein (PGBM; P98160). These proteins were increased in cases with DS, whereas protein IBP‐1 (P08833) was decreased by 40% compared with chromosomally normal fetuses. Four proteins, CO1A1, CO3A1, CO5A1, and PGBM, appeared as fragments. As differentially expressed proteins were present in all pregnancies with DS tested, they may represent useful potential markers for prenatal diagnosis. However, for protein biomarkers to be of any clinical utility, systematic analysis of the maternal serum should be conducted.
Audio indexing for an interactive Italian literature management system

A generic audio-based multimedia indexing and retrieval framework is presented. This work is mainly finalized to the development of various digital archives and technologies focused on the creation of a Content Management System (CMS) for Italian Literature specialized on searching, reading and listening. The main general objectives, among others more specific, are: the promotion of reading and listening Italian literature, the spreading of Italian oral narrative art and the design of new interactive communication tools and interfaces.
Kinetics and Frequency of Adeno-Associated Virus Site-Specific Integration into Human Chromosome 19 Monitored by Quantitative Real-Time PCR

ABSTRACT Adeno-associated virus type 2 (AAV-2) integrates specifically into a site on human chromosome 19 (chr-19) called AAVS1. To study the kinetics and frequency of chr-19-specific integration after AAV infection, we developed a rapid, sensitive, and quantitative real-time PCR assay for AAV inverted terminal repeat-chr-19-specific junctions. Despite the known variability of junction sites, conditions were established that ensured reliable quantification of integration rates within hours after AAV infection. The overall integration frequency was calculated to peak at between 10 and 20% of AAV-infected, unselected HeLa cells. At least 1 in 1,000 infectious AAV-2 particles was found to integrate site specifically up to day 4 postinfection in the absence of selection. Chromosomal breakpoints within AAVS1 agreed with those found in latently infected clonal cell lines and transgenic animals. Use of this quantitative real-time PCR will greatly facilitate the study of the early steps of wild-type and recombinant AAV vector integration.
Alles eine Frage hoher Reichweite? Eine experimentelle Untersuchung zur Ursache der Entstehung von Hostile-Media-Effekten

Dem Hostile-Media-Effekt zufolge sehen Personen, die eine bestimmte Meinung zu einem Thema haben, die mediale Berichterstattung dazu als tendenziell entgegengesetzt zu ihren eigenen Ansichten. Im vorliegenden Beitrag wird ein Erklarungsmodell fur den Effekt vorgeschlagen, wonach kontroverse Berichte die Gruppenzugehorigkeit involvierter Rezipienten aktivieren. Dabei sind Rezipienten gewahr, dass die mediale Berichterstattung von einer Masse an Menschen verfolgt wird. Daran, so die Annahme, knupft sich die Befurchtung, die Masse wurde durch die Berichterstattung negativ beeinflusst, indem der Standpunkt von Fremdgruppen gestarkt werde. Die Befurchtung resultiert in einer feindselig-verzerrten Wahrnehmung objektiv ausgewogener Medienberichte. Werden Informationen hingegen nicht massenmedial, sondern an ein lokales Publikum verbreitet, sollte ein kontrovers angelegter Medienbeitrag eher als die eigenen Gruppenansichten stutzend interpretiert werden. In einer experimentellen Studie wurden 230 Studierende um Einschatzungen zu einem Text uber Studiengebuhren gebeten. Der Text wurde entweder als Zeitungsartikel mit hoher Reichweite oder als lokal veroffentlichtes Produkt mit niedriger Reichweite prasentiert. Der lokal verbreitete Text wurde dabei erwartungsgemas als tendenziell mit der eigenen Meinung ubereinstimmend aufgefasst. Der Zeitungsartikel-Text wurde jedoch nicht als der eigenen Meinung entgegensetzt wahrgenommen. Die Ergebnisse werden auch vor dem Hintergrund moglicher anderer postulierter Einflussfaktoren wie der Wahrnehmung einer sozialen Distanz zum Mit-Publikum diskutiert.
Comparison of recall and cancer detection rates for immediate versus batch interpretation of screening mammograms.

PURPOSE To retrospectively compare recall and cancer detection rates between immediate and subsequent batch methods for interpretation of screening mammograms. MATERIALS AND METHODS Institutional review board approval was obtained, and informed consent was waived. Retrospective analysis was performed for 8698 screening mammograms obtained between January 1 and October 31, 2001, which were interpreted either immediately (n = 4113) or subsequently with batch method (n = 4585). Data were collected from data reporting system and patient billing records. Patients with high risk factors were excluded; 3441 patients were in the immediate group, and 3932 were in the batch group. The two groups were compared with respect to age, breast density, and availability of comparison films with Wilcoxon rank sum test. Recall rates and cancer detection rates for each group were determined and compared with Pearson chi(2) test; false-negative rates were compared with Fischer exact test. RESULTS A significant difference (P < .001) was noted in recall rates between immediate (18%) and batch (14%) groups; however, no significant difference (P = .7) was noted in cancer detection rates (immediate, 0.5%; batch, 0.4%). Mean age of patients was 56.8 years (age range, 21-96 years) in the immediate group and 56.2 years (age range 24-98 years) in the batch group (P = .02). Comparison of breast densities between groups indicates no statistically significant difference (P = .4). The batch group had significantly fewer comparison mammograms (3106 [79%]) available than the immediate group (2856 [83%]) (P < .001). There was no significant difference in false-negative rates between the immediate group (0.1%) and the batch group (0.1%) (P > .99). CONCLUSION Immediate interpretation of screening mammograms resulted in a statistically significant increase in recalls and additional clinical work-ups of perceived abnormalities; however, no significant difference in cancer detection rate was detected between groups.
Sphalerons, spectral flow, and anomalies

The topology of configuration space may be responsible in part for the existence of sphalerons. Here, sphalerons are defined to be static but unstable finite-energy solutions of the classical field equations. Another manifestation of the nontrivial topology of configuration space is the phenomenon of spectral flow for the eigenvalues of the Dirac Hamiltonian. The spectral flow, in turn, is related to the possible existence of anomalies. In this review, the interconnection of these topics is illustrated for three particular sphalerons of SU(2) Yang–Mills–Higgs theory.
EXPLORING THE SOCIALLY ANXIOUS BRAIN

Social anxiety disorder (SAD) is a prevalent psychiatric condition, which causes considerable suffering. The disorder has for long been studied in neuroscience, although the clinical impact of research results have so far been insignificant. In the first part of this essay, the basic understanding of SAD within cognitive neuroscience is provided. Studies using functional magnetic resonance imaging (fMRI)​ have revealed that SAD is primarily related to dysfunctions in, and between, threat processing, emotional regulatory, attentional and perceptual neural systems implicating regions such as the amygdala, insula, prefrontal, parietal and occipital lobes in the disorder​. To this background follows a presentation and discussion about more recent research on SAD using a neuroimaging method known as functional connectivity. Here, I find that the functional connectivity research, although problematic in many regards, extends the cognitive neuroscientific view on SAD. This by suggesting that the disorder is related to abnormalities in functional connectivity between several of the above-mentioned regions and within brain networks such as the default mode network. Finally, I explore the potential of functional connectivity as a tool for the diagnosis of SAD and for predicting individual patients' treatment responses. Studies on these topics, while sparse, indicate that functional connectivity measures can make both accurate classifications of SAD and predictions of treatment outcomes on the level of individuals. However, there is not sufficient empirical evidence to suggest that functional connectivity measures are superior to other neuroimaging measures in these contexts. Moreover, there are substantial challenges that need to be surmounted before neuroimaging measures can have clinical viability.
An atypical strain of Pasteurella gallinarum: pathogenic, phenotypic, and genotypic characteristics.

The pathogenicity of a strain of Pasteurella gallinarum isolated in Fresno County, Calif. , was compared with the American Type Culture Collection (ATCC) strain. Broiler chickens were inoculated intranasally with 10(7) colony-forming units (CFU) and intramuscularly with 10(5) CFU of each strain. The only notable lesions were in chickens inoculated intramuscularly with 10(5) CFU of the Fresno strain, which developed severe myositis at the inoculation site, pericarditis, perihepatitis, airsacculitis, and synovitis. P. gallinarum was reisolated from these lesions. Phenotypic characteristics of the two strains were identical except in reactions in ONPG broth and fermentation of xylose. Protein-banding patterns for the two strains were identical except for a single band difference in the 35-kilodalton region. Restriction endonuclease analysis confirmed that the Fresno strain was a distinct one. Plasmid analysis revealed that the ATCC strain had two plasmids and the Fresno strain had none.
Adenosine receptor antagonism affects regional resting vascular resistance during rat peritoneal sepsis.

BACKGROUND To identify vascular beds where endogenous adenosine plays a significant role as a mediator of resting perfusion alterations associated with sepsis, we tested the hypothesis that adenosine receptor blockade would cause differential regional increases in vascular resistance during intraperitoneal (ip) sepsis in the rat. MATERIALS AND METHODS Rats (250-350 g) were catheterized and randomized to septic or nonseptic groups. Sepsis was induced with an ip injection of cecal slurry (150 mg/kg in D5W; 5 ml/kg), and baseline hemodynamics, cardiac output (CO), and blood flows (microspheres) were measured 24 h later. Animals then received the adenosine receptor antagonist 8-phenyltheophylline (8-PTH; 10 mM, 1.5 ml/kg), its vehicle (1.5 ml/kg), or normal saline (1.5 ml/kg), iv, and measurements were repeated. RESULTS Septic animals treated with 8-PTH had a significant increase in skeletal muscle, hepatic portal, and cerebral vascular resistance with concomitant decreases in CO when compared with vehicle at 1 min. No significant resistance changes were observed in the renal, adipose, or coronary vasculatures. Adenosine receptor blockade caused a significant increase in +dP/dt and -dP/dt during sepsis, indicating that the reduced CO was not secondary to myocardial depression. CONCLUSIONS These data suggest that adenosine receptor-mediated actions during sepsis affect vascular beds selectively and indicate a significant role for adenosine in resting perfusion redistribution in sepsis.