gebhart/patrepeval huggingface dataset:
A Multidimensional Classification Approach for the Automated Analysis of Flow Cytometry Data (2008)

We describe an automated multidimensional approach for the analysis of flow cytometry data based on pattern classification. Flow cytometry is a widely used technique both for research and clinical purposes where it has become essential for the diagnosis and follow up of a wide spectrum of diseases, such as HIV-infection and neoplastic disorders. Flow cytometry data sets are composed of quite a large number of observations that can be viewed as elements of a n-dimensional space. The aim of the analysis of such data files is typically to classify groups of cellular events as specific populations with biological meaning. Despite significant improvements in data acquisition capabilities of flow cytometers, data analysis is still based on bi-dimensional strategies which were defined a long time ago. These are strongly dependent on the expertise of an expert operator, this approach being relatively subjective and potentially leading to unreliable results. Automated analysis of flow cytometry data is an essential step to improve reproducibility of the results. The proposed automated analysis was implemented on peripherial blood lymphocyte subsets from 307 samples stained and prepared in an identical way and it was capable of identifying all cell subsets present in each sample studied that could also be detected in the same data files by an expert operator. A highly significant correlation was found between the results obtained by an expert operator using a conventional manual method of analysis and those obtained using the implemented automated approach.
Prevalence, incidence and carrier frequency of 5q–linked spinal muscular atrophy – a literature review (2017)

Spinal muscular atrophy linked to chromosome 5q (SMA) is a recessive, progressive, neuromuscular disorder caused by bi-allelic mutations in the SMN1 gene, resulting in motor neuron degeneration and variable presentation in relation to onset and severity. A prevalence of approximately 1-2 per 100,000 persons and incidence around 1 in 10,000 live births have been estimated with SMA type I accounting for around 60% of all cases. Since SMA is a relatively rare condition, studies of its prevalence and incidence are challenging. Most published studies are outdated and therefore rely on clinical rather than genetic diagnosis. Furthermore they are performed in small cohorts in small geographical regions and only study European populations. In addition, the heterogeneity of the condition can lead to delays and difficulties in diagnosing the condition, especially outside of specialist clinics, and contributes to the challenges in understanding the epidemiology of the disease. The frequency of unaffected, heterozygous carriers of the SMN1 mutations appears to be higher among Caucasian and Asian populations compared to the Black (Sub-Saharan African ancestry) population. However, carrier frequencies cannot directly be translated into incidence and prevalence, as very severe (death in utero) and very mild (symptom free in adults) phenotypes carrying bi-allelic SMN1 mutations exist, and their frequency is unknown. More robust epidemiological data on SMA covering larger populations based on accurate genetic diagnosis or newborn screening would be helpful to support planning of clinical studies, provision of care and therapies and evaluation of outcomes.
Human Serum Contains N-Acetyflactosamine : β1–3 N-Acetylglucosaminyltransferase Activity (1984)

Human serum was shown to contain N-acetyllactosamine: N-acetylglucosaminyltransferase activity. The reaction product was hydrolyzed by beta-N-acetylglucosaminidase and released [14C]N-acetylglucosamine, indicating that the N-acetylglucosaminyl residue was beta-linked to N-acetyllactosamine. Methylation and hydrolysis of the reaction product yielded 2,4,6-trimethyl[3H]galactose, indicating that the N-acetylglucosaminyl residue was introduced at position C-3 of the terminal galactose of N-acetyllactosamine. In our experiments, 2,3,4-trimethyl[3H]galactose was not detected. Substrate competition studies between N-acetyllactosamine and lactose showed that this enzyme also catalyzed the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to lactose. Since the Km value for N-acetyllactosamine, which was 7.0 mM, was approximately a fourth of that for lactose (29.8 mM), N-acetyllactosamine was more effective than lactose as an acceptor.
The influence of Celecoxib on matrix synthesis by chondrocytes under mechanical stress in vitro (2005)

To assess effects of Celecoxib, selective cyclo-oxygenase (COX)-2 inhibitor, on matrix synthesis by chondrocytes under mechanical stress in vitro. Chondrocytes from 7-day-old rat articular cartilage were cultured. Cyclic mechanical stress (0.5 Hz, 7% elongation) was loaded using a Flexercell strain unit in the presence of Celecoxib, Indomethacin, and Ketoprofen. Concentrations of chondroitin sulfate (CS) in culture media were measured by high-performance liquid chromatography. Nitric oxide (NO) formation was detected by measuring NO2-accumulation in culture supernatants during the Griess reaction, using sodium nitrite as a standard. Levels of mRNA for aggrecan (AGC), type II collagen (CII), COX-2, and membrane-associated prostaglandin E synthase-1 (mPGES-1) were measured using real time reverse transcriptase-polymerase chain reaction. Under mechanical stress, levels of AGC and CII mRNA were decreased, while COX-2 mRNA levels were increased. Of the three drugs tested, only Celecoxib prevented the decrease of AGC mRNA and inhibited the release of CS. In addition, Celecoxib suppresses the level of mPGES-1 mRNA. These findings show that excessive mechanical stress decreases synthesis of matrix components in chondrocytes through a NO-regulated pathway, and suggest that Celecoxib has a protective effect on matrix metabolism.
Performance analysis and power allocation for M-QAM cooperative diversity systems (2010)

An adaptive regenerate and forward cooperative diversity (CD) system using quadrature amplitude modulation (QAM) for a two-user cooperation is proposed. The proposed system can achieve a maximum diversity order of two. The bit error probability (BEP) of a CD system depends primarily on the quality of the inter-user channel and user-to-destination channels, and the transmitted power of the cooperating users. Expressions which characterize the asymptotic behavior of the BEP as a function of the received signal-to-noise ratio (SNR) at the relay and the destination are derived. The transmit power is allocated optimally between the source and the relay according to the channel qualities and the CD system employed to achieve a prescribed BEP. Three power allocation strategies, each for a specific wireless communication scenario, which optimize the power consumption of the proposed CD system are introduced. The cooperative region, corresponding to each power allocation scheme, within which the partners must be located in order to yield a specified cooperative energy gain, is determined.
Position Sensing System Using Point Source of Light for Curved Micro-tunneling. (2000)

Curved micro-tunneling using small conduit pipes with diameters of 1m or less is recently applied in many construction sites. A new position sensing system to pinpoint the head of the first pipe has been come up with even when it cannot be seen directly from the base position. It differs from the traditional method of using the collimated laser beam, in that the diode laser with a large divergence is used as a point source of light and the direction of the point source of light is detected by using an objective lens and CCD camera. To apply this method to the position detection of the first pipe, the structure of the sensing unit and its detection accuracy were examined and the following results were obtained. (1) The structure using polarized beam splitter can suppress error led by rotating the sensing unit. (2) Through the simulation and some field tests, 20 seconds or less detection accuracy of direction angle was achieved.
Mycobacterium avium with the bird type IS1245 RFLP profile is commonly found in wild and domestic animals, but rarely in humans (2005)

Cervical lymphadenitis is the main manifestation of Mycobacterium avium infection in immunocompetent children. Exposure to birds has been discussed as a source of infection. To clarify from where children acquire the infection, M. avium isolates from different origins were analysed with restriction fragment length polymorphism (RFLP) on insertion sequence IS1245, and compared by computer cluster correlation analysis. This molecular epidemiological tool has previously revealed a distinction between multiband profiles found mainly in strains from humans, and a 3-band/bird type profile in strains isolated mainly from birds. 32 isolates from children were compared with 28 isolates from adults and 45 isolates from animals. We found that 67% of the animal isolates had the bird type profile, also found in 1 sputum isolate from an adult. Strains from children showed only multiband profiles that did not differ significantly from profiles of isolates from adults. All but 2 bird isolates showed the bird type profile. Neither of the remaining 2, which had multiband profiles, clustered with the isolates from children. Our results indicate that the true reservoir of M. avium is unknown. Thus the question of whether or not M. avium can be incriminated as a zoonotic disease remains unanswered.
Small molecule antagonists for chemokine CCR3 receptors (2009)

The chemokine receptor CCR3 is believed to play a role in the development of allergic diseases such as asthma, atopic dermatitis, and allergic rhinitis. Despite the conflicting results that have been reported regarding the importance of eosinophils and CCR3 in allergic inflammation, inhibition of this receptor with small molecule antagonists is thought to provide a valuable approach for the treatment of these diseases. This review describes the structure-activity relationships (SAR) of small molecule CCR3 antagonists as reported in the scientific and patent literature. Various chemical classes of small molecule CCR3 antagonists have been described so far, including (bi)piperidine and piperazine derivatives, N-arylalkylpiperidine urea derivatives and (N-ureidoalkyl)benzylpiperidines, phenylalanine derivatives, morpholinyl derivatives, pyrrolidinohydroquinazolines, arylsulfonamides, amino-alkyl amides, imidazole- and pyrimidine-based antagonists, and bicyclic diamines. The (N-ureidoalkyl)benzylpiperidines are the best studied class in view of their generally high affinity and antagonizing potential. For many of these antagonists subnanomolar IC(50) values were reported for binding to CCR3 along with the ability to effectively inhibit intracellular calcium mobilization and eosinophil chemotaxis induced by CCR3 agonist ligands in vitro.
6,6-Difluoro-19-norprogesterone (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT6,6-Difluoro-19-norprogesteroneAlexander L. JohnsonCite this: J. Med. Chem. 1972, 15, 7, 784–785Publication Date (Print):July 1, 1972Publication History Published online1 May 2002Published inissue 1 July 1972https://pubs.acs.org/doi/10.1021/jm00277a023https://doi.org/10.1021/jm00277a023research-articleACS PublicationsRequest reuse permissionsArticle Views39Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Primal-dual coding to probe light transport (2012)

Figure 1: Left to right: Scene under white illumination, global illumination component captured in just a single RAW photograph (no processing), and direct component from subtracting the middle image from the left image. The global image was captured using 512 primal and dual patterns during one 30-second exposure. Notice that the objects embedded within the wax disk are only visible in the global image. We present primal-dual coding, a photography technique that enables direct fine-grain control over which light paths contribute to a photo. We achieve this by projecting a sequence of patterns onto the scene while the sensor is exposed to light. At the same time, a second sequence of patterns, derived from the first and applied in lockstep, modulates the light received at individual sensor pixels. We show that photography in this regime is equivalent to a matrix probing operation in which the elements of the scene’s transport matrix are individually re-scaled and then mapped to the photo. This makes it possible to directly acquire photos in which specific light transport paths have been blocked, attenuated or enhanced. We show captured photos for several scenes with challenging light transport effects, including specular inter-reflections, caustics, diffuse inter-reflections and volumetric scattering. A key feature of primal-dual coding is that it operates almost exclusively in the optical domain: our results consist of directly-acquired, unprocessed RAW photos or differences between them.
Designing a new test for contrast sensitivity function measurement with iPad (2014)

The new ClinicCSF application for iPad retina showed no significant differences with FACT test when the same contrast sensitivity steps were used. In addition, it is shown that the accurateness of a vision screening could be improved with the use of an appropriate psychophysical method.
Rainbow scattering by a coated sphere (1994)

We examine the behavior of the first-order rainbow for a coated sphere by using both ray theory and Aden-Kerker wave theory as the radius of the core a(12) and the thickness of the coating δ are varied. As the ratio δ/a(12) increases from 10(-4) to 0.33, we find three classes of rainbow phenomena that cannot occur for a homogeneous-sphere rainbow. For δ/a(12) ≲ 10(-3), the rainbow intensity is an oscillatory function of the coating thickness, for δ/a(12) ≈ 10(-2), the first-order rainbow breaks into a pair of twin rainbows, and for δ/a(12) ≈ 0.33, various rainbow-extinction transitions occur. Each of these effects is analyzed, and their physical interpretations are given. A Debye series decomposition of coated-sphere partial-wave scattering amplitudes is also performed and aids in the analysis.
The Clinical Efficacy of Digitized Film-Screen Mammograms (2010)

Background and purpose: The purpose of this study was to examine differences in interpretation between film-screen mammograms (FSMs) and digitized FSMs (DFSMs). Materials and Methods: Samples included a randomly selected group of 100 patients with mammograms, all of which were digitized to digital data. Each mammogram included the 2 standard craniocaudal and mediolateral oblique films. All of the mammograms were scanned using a digitizer, and then transferred onto a Picture Archiving and Communication System server. All of the FSMs and DFSMs were interpreted by 2 specialized radiologists in terms of the lesion location, characteristics, and Breast Imaging Reporting and Data System (BI-RADS). The reading sessions for each of the 2 groups of mammograms were separated by a period of 4weeks. Results: The results showed there was no difference in the BIRADS, location, or characteristics of microcalcifications and tumors between FSMs and DFSMs. Results of the interpretation between the 2 radiologists were similar with no significant differences. Conclusions: The efficacy of DFSMs equals that of FSMs.
1.8THz receiver development for the TELIS instrument (2005)

A new state-of-the-art balloon borne three channel (500GHz,
625GHz, 1.8 THz) cryogenic heterodyne spectrometer will allow
enhanced limb sounding of the Earth's atmosphere within the
submillimeter and far-infrared spectral range. The instrument,
called TELIS (TErahertz and submm LImb Sounder), is being
developed by a consortium of major European institutes that
includes the Space Research Organisation of the Netherlands
(SRON), the Rutherford Appleton Laboratory (RAL) in the United
Kingdom and the Deutschen Zentrum fur Luft- und Raumfahrt (DLR) in
Germany (lead institute). TELIS will utilise state-of-the-art
superconducting heterodyne technology and is designed to be
compact and lightweight, while providing broad spectral coverage,
high spectral resolution and long flight duration. Target species
are key atmospheric short-lived radicals such as OH, HO2, ClO,
BrO together with stable constituents such as O3, HCl and HOCl.
TELIS will consist of a common front end with a cassegrain based
pointing telescope, common transfer optics and a digital
autocorrelator spectrometer for each channel.

One of the three receiver channels (developed by DLR) will focus
on the measurement of the OH-triplett at 1.8 THz. Low noise NbN
based Hot Electron Bolometers will be acting as heterodyne mixing
elements. A Martin Puplett Interferometer designed for cryogenic
operation in the cryostat is used to interfer signal- and LO
radiation generated by a solid state based local oscillator unit.

Recently athe laboratory DSB version of the TELIS heterodyne receiver
(using a far infrad laser as preliminary LO source) has been set
up and tested successfully. In this paper the current status of
the THz-channel design and development in the framework of the
TELIS project will be presented.
Identification and characterization of diverse OTU deubiquitinases in bacteria (2020)

ABSTRACT Manipulation of host ubiquitin signaling is becoming an increasingly apparent evolutionary strategy among bacterial and viral pathogens. By removing host ubiquitin signals, for example, invading pathogens can inactivate immune response pathways and evade detection. The Ovarian Tumor (OTU) family of deubiquitinases regulates diverse ubiquitin signals in humans. Viral pathogens have also extensively co-opted the OTU fold to subvert host signaling, but the extent to which bacteria utilize the OTU fold was unknown. We have predicted and validated a set of OTU deubiquitinases encoded by several classes of pathogenic bacteria. Biochemical assays highlight the ubiquitin and polyubiquitin linkage specificities of these bacterial deubiquitinases. By determining the ubiquitin-bound structures of two examples, we demonstrate the novel strategies that have evolved to both thread an OTU fold and to recognize a ubiquitin substrate. With these new examples, we perform the first cross-kingdom structural analysis of the OTU fold that highlights commonalities among distantly-related OTU deubiquitinases.
Analysis on genetic contribution of some traits to seed yield in rapeseed by additive-dominance genetic method of mixed model (2010)

Analysis on genetic contribution of some traits to seed yield in rapeseed by additive-dominance genetic method of mixed model A genetic model is developed with additive, dominance and genotype x environment interaction effects for the progeny from a diallel mating design. To uncover the genetic contributions of some traits of rapeseed to seed yield and find indicator traits for indirect selection, multivariable conditional analysis was conducted based on this method. Therefore, an experiment was conducted to estimate genetic parameters using a half diallel of nine international rapeseed cultivars. The 36 Fl hybrids, the parents and four additional cultivars were planted in the breeding nurseries in 2008 and 2009. Several traits including number of pods per plant (NPP), pod length (LP), height of the first pod (HFP), height of the first lateral branch (HFB), stem diameter (SD), days of flowering period (FP), days to physiological maturity (DPM) and seed yield were recorded. The genetic variance component (V DxY ) was significant for all the studied traits but the genetic variance component (V A ) was significant for NPP, HFB, HFP, DPM and SY traits and the genetic variance component (V D ) was significant for HFB, HFP, LP and FP traits. There was significant positive phenotypic correlation (r A ) between seed yield with NPP and HFP and there was significant positive dominance x year interaction correlation (r DxY ) between seed yield with NPP and DPM while there was significant negative dominance x year interaction correlation (r DxY ) between seed yield with HFB, LP and FP. There were significantly positive additive effects of SY for two parents Orient and Talaye. Finally according to additive-dominance genetic model and conditional genetic effects, the genotypes Talaye proved good general combiner for seed yield improvement and crosses 4 × 8 (Orient × Talaye), 7 × 8 (Opera × Talaye) were found the best specific combiner for all the studied traits.
Integrated Care and Leprosy in India:A Role for Indian Systems of Medicine and Traditional Health Practice in the Eradication of Leprosy (2016)

The benefits of an integrated approach in the future of leprosy control in India are discussed, by involving professionals from different systems of medicine and coordinated by dermatologists working in the field of community dermatology. The low level of education amongst traditional healers has led to misdiagnosis and inappropriate treatment, thus emphasizing the importance of health education for patients, families and local practitioners to enable prompt and appropriate treatment. The Indian systems of medicine though supportive do not have the required rehabilitation services. Traditional health practitioners demonstrated an improved knowledge of leprosy on completion of training, and were able to detect and refer suspect cases with only early signs of disease.
Bacterial resistance to tetracycline: mechanisms, transfer, and clinical significance (1992)

Tetracycline has been a widely used antibiotic because of its low toxicity and broad spectrum of activity. However, its clinical usefulness has been declining because of the appearance of an increasing number of tetracycline-resistant isolates of clinically important bacteria. Two types of resistance mechanisms predominate: tetracycline efflux and ribosomal protection. A third mechanism of resistance, tetracycline modification, has been identified, but its clinical relevance is still unclear. For some tetracycline resistance genes, expression is regulated. In efflux genes found in gram-negative enteric bacteria, regulation is via a repressor that interacts with tetracycline. Gram-positive efflux genes appear to be regulated by an attenuation mechanism. Recently it was reported that at least one of the ribosome protection genes is regulated by attenuation. Tetracycline resistance genes are often found on transmissible elements. Efflux resistance genes are generally found on plasmids, whereas genes involved in ribosome protection have been found on both plasmids and self-transmissible chromosomal elements (conjugative transposons). One class of conjugative transposon, originally found in streptococci, can transfer itself from streptococci to a variety of recipients, including other gram-positive bacteria, gram-negative bacteria, and mycoplasmas. Another class of conjugative transposons has been found in the Bacteroides group. An unusual feature of the Bacteroides elements is that their transfer is enhanced by preexposure to tetracycline. Thus, tetracycline has the double effect of selecting for recipients that acquire a resistance gene and stimulating transfer of the gene.