Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential transcription of baculovirus late and very late promoters: fractionation of nuclear extracts by phosphocellulose chromatography

An in vitro transcription system based on cytidine-free cassette was developed for the late 39k gene and the very late polyhedrin gene of Autographa californica nuclear polyhedrosis virus (AcNPV). Optimization of transcription conditions revealed that a preincubation step was not required for transcription of late and very late promoters, although preincubation was essential for efficient transcription from an early promoter. The 39k and polyhedrin constructs were actively transcribed by nuclear extracts prepared from AcNPV-infected Spodoptera frugiperda cells at 12 or 36 h postinfection but not by nuclear extracts prepared from uninfected or infected cells harvested during the early phase of infection. Transcription from the very late polyhedrin promoter was fivefold higher than that from the 39k late promoter with the nuclear extract prepared at 36 h postinfection. The 36-h extract was fractionated by phosphocellulose chromatography. Transcription activity eluted in two fractions, at 0.3 and 0.5 M KCl. Both the 39k and polyhedrin constructs were transcribed by these fractions; however, the patterns of late and very late transcription were distinctly different. With the 0.3 M fraction, incorporation into the 39k transcript was approximately 10-fold higher than incorporation into the polyhedrin transcript. Alternatively, with the 0.5 M fraction, transcription of the polyhedrin construct was twofold higher than transcription of the 39k construct. These results indicate that this in vitro system will be useful for purification and identification of factors that discriminate between late and very late promoters.
Modification of the Threshold Equalising Noise (TEN) test for cochlear dead regions for use with steeply sloping high-frequency hearing loss

Steeply sloping high-frequency hearing loss is often associated with cochlear dead regions. These can be identified by measuring pure-tone thresholds in quiet and in Threshold-Equalising Noise (TEN). However, many patients cannot be adequately tested because the low frequencies in the TEN lead to uncomfortable loudness. We investigated the effect of high-pass filtering on the TEN-test results and the loudness of the TEN. Twenty-four normally hearing subjects and 35 subjects with steeply sloping high-frequency hearing loss were tested, using the standard TEN (TENs), and TEN high-pass filtered at 0.5 kHz (TEN0.5) or 1 kHz (TEN1). For both groups, masked thresholds did not differ across noise types for frequencies above 1 kHz. Over 50% of the hearing-impaired ears tested met the criteria for a dead region at 4 kHz, using all three noise types. However, masked thresholds and the prevalence of positive TEN-test results at 1 kHz were both lower with the TEN1. The TEN1 was judged the most comfortable noise by 68% of the hearing-impaired subjects. We conclude that high-pass filtering would allow testing at higher TEN levels for patients with steeply sloping hearing loss. Sumario La hipoacusia de perfil abruptamente descendente en frecuencias agudas se asocia frecuentemente con regiones cocleares muertas. Esto se puede identificar midiendo los umbrales tonales en silencio y en ruido ecualizado al umbral (TEN). Sin embargo, algunos pacientes no pueden ser estudiados adecuadamente porque las frecuencias bajas en el TEN, les produce molestia. Investigamos el efecto del filtro pasa-alto en los resultados de las pruebas TEN y la intensidad subjetiva del TEN. Se examinaron 24 sujetos normoyentes y 35 con hipoacusia de perfil abruptamente descendente en frecuencias agudas, utilizando el TEN habitual y el TEN con filtro pasa/alto a 0.5 kHz (TEN0.5) o 1 kHz (TEN1). Los umbrales de enmascaramiento no difirieron con los diferentes tipos de ruido para las frecuencias por arriba de 1 kHz en ambos grupos. Más del 50% de los oídos hipoacúsicos cumplieron con los criterios para considerar una zona muerta a 4 kHz, con los tres tipos de ruido. Sin embargo, los umbrales de enmascaramiento y la prevalencia de una prueba TEN positiva a 1 kHZ fueron menores con el TEN1. El 68% de los hipoacúsicos consideraron al TEN1 como el ruido más confortable. Concluimos que el filtro pasa-alto puede permitir realizar pruebas con mayor intensidad TEN en pacientes con hipoacusia de perfil abruptamente descendente en frecuencias agudas.
An acoustic examination of the three-way sibilant contrast in lower sorbian

Abstract The current paper presents an acoustic study of Lower Sorbian. Four native speakers of Lower Sorbian participated in this study. Center of gravity, standard deviation, skewness, kurtosis and slope measures were taken to measure the fricatives' spectral qualities. Vocalic transitions were also taken to gather finer grained information about the sibilants' articulation. The results indicated there is a three-way contrast in Lower Sorbian. The alveolar and retroflex segments have approximately the same place of articulation, but the overall tongue shape contributes significantly to the difference in spectral properties. The alveolopalatal segment is composed of a tongue-palate contact which extends from the dental place towards the palatal. This suggests that the length of the constriction also greatly affects the spectral properties of the fricatives. However, the phonetic realization of these segments is not the same as in Polish. The COG measures indicate both the Lower Sorbian retroflex and alveolopalatal segments is much lower than Polish. This suggests that the phonetic instantiation of the three-way contrast is variable. The results also indicate that the acoustic-perceptual cues from the vowel transitions and fricative spectra work in conjunction to distinguish the sibilants because no single cue is reliable enough to distinguish all of them.
Arctic and Arctic-like rabies viruses: distribution, phylogeny and evolutionary history

SUMMARY Forty-one newly sequenced isolates of Arctic and Arctic-like rabies viruses, were genetically compared to each other and to those available from GenBank. Four phylogenetic lineages of Arctic viruses were identified. Arctic-1 viruses circulate in Ontario, Arctic-2 viruses circulate in Siberia and Alaska, Arctic-3 viruses circulate circumpolarly, and a newly described lineage Arctic-4 circulates locally in Alaska. The oldest available isolates from Siberia (between 1950 and 1960) belong to the Arctic-2 and Arctic-3 lineages and share 98·6–99·2% N gene identity with contemporary viruses. Two lineages of Arctic-like viruses were identified in southern Asia and the Middle East (Arctic-like-1) and eastern Asia (Arctic-like-2). A time-scaled tree demonstrates that the time of the most recent common ancestor (TMRCA) of Arctic and Arctic-like viruses is dated between 1255 and 1786. Evolution of the Arctic viruses has occurred through a northerly spread. The Arctic-like-2 lineage diverged first, whereas Arctic viruses share a TMRCA with Arctic-like-1 viruses.
Preclinical Assessment of Therapeutic Antibodies against Human CD40 and Human Interleukin-12/23p40 in a Nonhuman Primate Model of Multiple Sclerosis

Background: Proinflammatory cytokines, such as interleukin (IL)-12 and IL-23, and costimulatory molecules on antigen-presenting cells (APC), such as CD40, are critical to autoreactive T cell activation by APC, and hence, are considered relevant targets of therapy for immune-mediated inflammatory diseases (IMID). Objective: The current review discusses the preclinical evaluation of two novel immunotherapeutic monoclonal antibodies (mAbs), one directed against human IL-12/23p40 and the other against CD40. As the antibodies only recognize their target molecule in primates, the efficacy could not be tested in rodent models. Results: As a preclinical IMID model for the in vivo evaluation of both mAbs, we have used the experimental autoimmune/allergic encephalomyelitis (EAE) model in common marmoset monkeys (Callithrix jacchus). Both mAbs show beneficial activities in the EAE model when administered early in disease development as well as after the onset of brain inflammation. The treatment effects were evaluated using a combination of quantitative magnetic resonance imaging and a series of ex vivo and immunopathological evaluations. Conclusion: The promising effects during ongoing disease in a relevant preclinical IMID model illustrate the potential of these two antibodies as treatment of IMID, in particular for multiple sclerosis on which disease EAE has been modeled.
Selected Arylpiperazines Are Capable of Reversing Multidrug Resistance in Escherichia coli Overexpressing RND Efflux Pumps

ABSTRACT Several arylpiperazines capable of reversing multidrug resistance (MDR) in Escherichia coli overexpressing acrAB and acrEF but not in pump-deficient mutant strains were identified. 1-(1-Naphthylmethyl)-piperazine, one of the more active compounds, enhanced susceptibility to fluoroquinolones and other agents and increased the intracellular concentration of levofloxacin and ethidium bromide, suggesting efflux pump inhibition as the mechanism of MDR reversal.
Cell‐Cell and Cell‐Extracellular Matrix Interactions Regulate Embryonic Stem Cell Differentiation

Cell interactions with the extracellular matrix (ECM) play a critical role in their physiology. Here, we sought to determine the role of exogenous and endogenous ECM in the differentiation of nonhuman primate ESCs. We evaluated cell differentiation from expression of lineage gene mRNA and proteins using real‐time polymerase chain reaction and immunohistochemistry. We found that ESCs that attached to and spread upon highly adhesive collagen do not differentiate efficiently, whereas on the less adhesive Matrigel, ESCs form aggregates and differentiate along mesoderm and especially endoderm lineages. To further decrease ESC attachment to the substrate, we cultured them either on nonadhesive agarose or in suspension. In both cases, ESCs formed aggregates and efficiently differentiated along endoderm and mesoderm lineages, most strikingly into cardiomyocytes. Aggregates formed by thus‐differentiated ESCs started to beat with a frequency of 50–100 beats per minute and continued to beat for approximately a month. In spite of the presence of exogenous ECM, ESCs were dependent on endogenous ECM for their survival and differentiation, as the inhibition of endogenous collagen induced a gradual loss of ESCs and neither a simple matrix, such as type I collagen, nor the complex matrix Matrigel was able to rescue these cells. In conclusion, adhesiveness to various ECM and nonbiological substrates determines the differentiation of ESCs in such a way that efficient cell‐cell aggregation, together with less efficient cell attachment and spreading, results in more efficient cell differentiation.
Prevalence and risk factors associated with retinopathy in diabetic patients at Parirenyatwa Hospital outpatients ’ clinic in Harare , Zimbabwe Pasipanodya

Diabetic retinopathy is the fifth leading cause of blindness worldwide accounting for nearly 5% of all blindness. However, most of the prevalence and incidence data is from developed countries, with very limited information from sub-Saharan Africa. The study sought to determine the prevalence of, and factors associated with, retinopathy in diabetic patients. Diabetes mellitus patients attending the outpatients’ clinic at Parirenyatwa Group of Hospitals between October 2013 and July 2014 were recruited into this analytical cross-sectional study. Demographic information was collected. A nurse carried out anthropometric measurements. An ophthalmologist using slit lamp indirect ophthalmoscopy with a 20-diopter and a 90-diopter lens diagnosed retinopathy. Blood samples were collected and analysed for triglycerides, total cholesterol, HDL cholesterol, glycosylated hemoglobin and serum creatinine. A total of 340 patients were enrolled into the study, of whom 73.2% were female. Mean (SD) age was 57.5 (14.9) years and there was no difference in age between females [57.6 (14.1) years] and males [57.2 (16.8) years]. The overall prevalence of diabetic retinopathy was 28.4%. Using multivariate logistic regression analysis retinopathy was associated with longer duration of diabetes mellitus (OR 1.06, 95% CI 1.03-1.09, p value ˂ 0.001) and lower serum creatinine (OR 0.99, 95% CI 0.97-1.00, p value 0.025). The prevalence of diabetic retinopathy was 28.4%. Longer duration of diabetes mellitus and lower serum creatinine, which is a marker of renal damage, were independent risk factors of diabetic retinopathy.
Deceit: a flexible distributed file system

Deceit, a distributed file system that provides flexibility in the fault-tolerance and availability of files, is described. Deceit provides many capabilities to the user: file replication with concurrent reads and writes, a range of update propagation strategies, automatic disk load balancing and the ability to have multiple versions of a file. Deceit provides Sun Network File Server (NFS) protocol compatibility; no change in NFS client software is necessary in order to use Deceit. The purpose of Deceit is to replace large collections of NFS servers. NFS suffers from several problems in an environment where most clients mount most servers. First, if any one server crashes, clients will block or fail when they try to access that server, and, as the number of servers increases, this problem becomes more likely. Second, servers have a (roughly) fixed capacity, yet it is difficult to move files from one NFS server to another without disrupting clients. Third, replicating a file to increase its availability must be managed by the user. Deceit addresses these three problems. <<ETX>>
UvA-DARE ( Digital Academic Repository ) Correlation between fast quasi-periodic oscillations and X-ray spectral shape in atoll sources

We present correlations between the frequency of the fast quasi-periodic oscillations (QPOs) and the shape of the X-ray spectrum in the atoll sources 4U 1608252 and 4U 06141091. We find that the photon index of a power-law component of the energy spectrum is well correlated with the QPO frequency in both sources. The correlation between the photon index and the QPO frequency most likely represents a common dependence on some physical parameter of the system. Subject headings: accretion, accretion disks — stars: individual (4U 06141091, 4U 1608252) — stars: neutron — X-rays: stars
Noncommutative Sinkhorn theorem and generalizations

Our topic traces back to DEMING AND STEPHAN [1] who sought to reconcile an empirical joint distribution of two random variables with a priori known marginals for each and proposed an iterative scheme for determining a solution. Thus, in the case of finite probability spaces, the problem data consist of two probability vectors p0 and p1 together with the empirical joint probability matrix P = [p(i, j)], i.e., a matrix P such that p(i, j) ≥ 0 and ∑ i,j p(i, j) = 1. Then the task is to suitably modify P into P̂ = [p(i, j)] which is consistent with the marginals, i.e., ∑
Nucleotide sequence of the tetracycline resistance gene of pBC16 from Bacillus cereus.

pBC16 is a commonly used tetracycline resistance (TcR) plasmid originating from B. cereus (1). The tet gene of the plasmid is also expressed in Escherichia coli. By restriction analysis pBC16 has been shown to be closely related to other TcR plasmids of Bacillus origin (2), to the Streptococcus faecalis TcR plasmid pAMcal and to the Staphylococcus aureus plasmid pUB110 which, however, carries a kanamycin resistance gene instead of the tet gene (3). We isolated pBC16 from Bacillus subtilis (natto) 3335, kindly provided by Dr. Thome (4), and sequenced both strands from the region of the tet-gene by the method of Sanger et al. (5). Nucleotides underlined in the sequence correspond to putative -35 and -10 regions, to two consensus Shine-Dalgarno sequences of open reading frames for a leader peptide and the TcR-protein and their translational start and stop codons and to a Rho-independent transcriptional terminator. Computer analysis of homologous sequences revealed that the tet-gene of pBC16 is almost identical with those of pTHT15 and pLSl, isolated from a thermophilic Bacillus (6) and Streptococcus agalactiae (7), respectively. Only two nucleotides, at the promoter and leader region, differ in the tet genes of pBC16 and
Joint source-channel coding over Gaussian channels with intersymbol interference using tree structured vector quantization

The transmission of a vector quantized Markov source over channels with intersymbol interference (ISI) using M-dimensional modulation procedures is considered. The source is quantized using a channel matched tree structured vector quantizer (CM-TSVQ) in which the VQ design is performed with respect to channel error matrices computed by simulation. The CM-TSVQ is combined with a recursive block MAP receiver that provides soft decisions and accounts for the residual redundancy left at the vector quantizer output. In order to reduce the complexity of the decoding, computation in the log-domain of the probability metrics is used. The M-dimensional modulation is implemented as M/2 two-dimensional QAM. Optimum power allocation between QAM signal sets is determined. Results are presented for the case of two stage TSVQ, using 2-QAM, and are compared to the OPTA (optimum performance theoretically attainable) bound for Gaussian channel with and without ISI.
Multi-dimensional electron microscopy.

The complexity of modern structural and functional materials requires high spatial resolution characterisation in all 3 dimensions. Over the past 15 years or so, electron tomography (3D imaging) has become established as a near-routine tool for the 3D study of materials. Early electron tomography used many of the ideas and methods established first in the life sciences, using a tilt series of bright-field (BF) images acquired by rotating the sample about a single axis and recording images every 1-2°. For many materials problems, however, BF images may not be ideal and the introduction of STEM HAADF tomography offered materials microscopists an imaging mode that, in many cases, is much more suited for tomography, providing images with greatly reduced diffraction contrast, with a signal that in most cases varies monotonically with thickness (satisfying the projection requirement) and providing compositional contrast through the atomic number (Z) dependence of the high angle (Rutherford-like) scattering [1-3]. Following on from weak beam tomography methods, STEM tomography (both BF and ADF) has been developed for the study of defects (especially dislocations) where a reconstruction (or 3D representation) of the dislocation can be simplified to lines running through space.
Segmentation Free Nastalique Urdu OCR

Electronically available Urdu data is in image form which is very difficult to process. Printed Urdu data is the root cause of problem. So for the rapid progress of Urdu language we need an OCR system, which can help us to make Urdu data available for the common person. Research has been carried out for years to automate Arabic and Urdu script. But the biggest hurdle in the development of Urdu OCR is the challenge to recognize Nastalique Script which is taken as standard for writing Urdu language. Nastalique script is written diagonally with no fixed baseline which makes the script somewhat complex. Overlap is present not only in characters but in the ligatures as well. This paper proposes a method which allows successful recognition of Nastalique Script.
Sonographic Appearance of the Gallbladder in the Allogeneic Hematopoietic Stem Cell Transplant Population

To determine whether gallbladder sonographic findings in hematopoietic stem cell (HSC) transplant patients can distinguish among hepatobiliary complications of HSC transplants (graft‐versus‐host disease [GVHD] and veno‐occlusive disease) and biliary events (cholecystitis, cholangitis, and choledocholithiasis).
Microstructures of SiC nanoparticle-doped MgB2∕Fe tapes

We have studied bulk MgB2 synthesized by reaction of MgH2 and B with and without SiC nanoparticles and at a range of reaction temperatures. All of the samples showed enhanced upper critical fields compared to most bulk MgB2, including the sample with 10at. % SiC reacted at 600°C, which showed Hc2(0K)>42T. Extensive transmission electron microscopy (TEM) and STEM observations show that using MgH2 instead of pure Mg reduces the concentration of oxide second phases in the tapes, but that adding SiC reintroduces nanoscale grains of MgO, SiO2, and SiOxCy, and larger grains of Mg2Si. SiC causes some C doping of the MgB2, but electron energy loss spectroscopy and x-ray diffraction measurements show that the C concentration is similar to other bulk C-doped MgB2. In all the samples with and without SiC, the grain size is very small, 10–60nm. Electron scattering from the high density of grains and second-phase boundaries is responsible for the enhanced Hc2 of these samples. However, the Hc2 properties are somewhat c.
CD4 T cell memory derived from young naive cells functions well into old age, but memory generated from aged naive cells functions poorly

Age-related declines in immune function have an impact on both primary and memory responses. In this study, we have examined the ability of naive CD4 T cells from young and aged T cell receptor transgenic mice to establish functional memory. We found that memory cells generated from young CD4 T cells responded well to antigen, even a year after generation, whereas memory cells derived from CD4 T cells from aged mice responded poorly both ex vivo and in vivo. Memory cells generated from aged naive cells proliferate less, produce reduced levels of cytokines, and exhibit reduced cognate helper function, compared with memory cells generated by using young naive cells. These results indicate that it is the age of the naive T cell when it first encounters antigen, rather than the age when it reencounters antigen, that is critical for good memory CD4 T cell function.
Impairments in activities of daily living in Parkinson's disease: implications for management.

Parkinson's disease (PD) is a neurodegenerative disorder with progressive impairment in motor and cognitive functioning. A review of past research shows that individuals experience not only physical discomfort brought on by the illness, but also considerable psychological distress. Increased dependency on a caregiver due to impairments in activities of daily living (e.g., walking, eating, dressing) may bring on feelings of being a burden and strain relationships. However, since PD is a chronic illness, it necessitates family caregiving throughout the life-span. This has implications for the family members who need to redefine their roles within the family to manage the circumstances brought on by the illness. Such strains may include finances, threats to employment, social isolation or health strain. Thus, it becomes imperative to provide unrelenting support to the affected family and individual, to enable them to refocus and learn to manage new illness-related, task-oriented, and affective roles. This enhances the integrity and self-esteem of the patient and helps the family's adjustment to illness of a member. This paper outlines, the role of mental health professionals in providing counseling and psychoeducational approaches to helping patients and their families.
Models Arising from a Flexible Manufacturing Machine, Part II: Minimization of the Number of Switching Instants

This paper deals with a job scheduling problem for a flexible manufacturing machine. We consider the same manufacturing environment described in a companion study Part I, but we use a different performance criterion: to minimize the total number of instants at which tools are switched. This performance criterion is appropriate when the switching time is roughly constant and independent of the number of tool switches. We show that this scheduling problem generalizes the classical bin packing problem, and we present a non-LP-based branch-and-bound procedure that terminates with an optimal solution. We extend this procedure to the case of K machines in sequence.