gebhart/patrepeval huggingface dataset:
Delivery of the Cas9 or TevCas9 System into Phaeodactylum tricornutum via Conjugation of Plasmids from a Bacterial Donor (2018)

Diatoms are an ecologically important group of eukaryotic microalgae with properties that make them attractive for biotechnological applications such as biofuels, foods, cosmetics and pharmaceuticals. <i>Phaeodactylum tricornutum</i> is a model diatom with defined culture conditions, but routine genetic manipulations are hindered by a lack of simple and robust genetic tools. One obstacle to efficient engineering of <i>P. tricornutum</i> is that the current selection methods for <i>P. tricornutum</i> transformants depend on the use of a limited number of antibiotic resistance genes. An alternative and more cost-effective selection method would be to generate auxotrophic strains of <i>P. tricornutum</i> by knocking out key genes involved in amino acid biosynthesis, and using plasmid-based copies of the biosynthetic genes as selective markers. Previous work on gene knockouts in <i>P. tricornutum</i> used biolistic transformation to deliver CRISPR-Cas9 system into <i>P. tricornutum</i>. Biolistic transformation of non-replicating plasmids can cause undesired damage to <i>P. tricornutum</i> due to random integration of the transformed DNA into the genome. Subsequent curing of edited cells to prevent long-term overexpression of Cas9 is very difficult as there is currently no method to excise integrated plasmids. This protocol adapts a new method to deliver the Cas9 or TevCas9 system into <i>P. tricornutum</i> via conjugation of plasmids from a bacterial donor cell. The process involves: 1) design and insertion of a guideRNA targeting the <i>P. tricornutum</i> urease gene into a TevCas9 expression plasmid that also encodes a conjugative origin of transfer, 2) installation of this plasmid in <i>Escherichia coli</i> containing a plasmid (pTA-Mob) containing the conjugative machinery, 3) transfer of the TevCas9 expression plasmid into <i>P. tricornutum</i> by conjugation, 4) screening of ex-conjugants for urease knockouts using T7 Endonuclease I and phenotypic screening, and 5) curing of the plasmid from edited cells.
Importance of CD34+ cell subsets in autologous PBSC transplantation: the mulhouse experience using CD34+CD38- cells as predictive tool for hematopoietic engraftment. (2001)

Over the years, various biological parameters have been proposed for predicting rapidity and long term maintenance of hematopoietic engraftment after peripheral blood stem cell transplantation (PBSCT). Determination of the graft content in CFU-GM was the only one available until the end of the eighties. But, for technical reasons, and also because it does not actually evaluate the self-renewal potential of the cell products reinfused, it has now been commonly replaced by the determination of CD34+ cell amounts, which are known to contain the pluripotent hematopoietic stem cells. However, a frequent discrepancy still exists between the number of CD34+ cells reinfused and the engraftment efficiency. We have recently demonstrated a higher accuracy of the numbers of CD34+38- cells contained in graft products to predict rapidity of trilineage engraftment, which has further been confirmed by other investigators. Furthermore, we and others, have proposed a threshold dose of 5 x 10(4) CD34+38- cells/kg b.w. below which the trilineage engraftment kinetics are significantly slower and unpredictible. This "cut-off" value also appears to be a realistic clinical tool to decide if hematopoietic growth factor(s) must be administered or not after PBSCT. Indeed, when for example, rh-G-CSF administration after transplant of CD34+38- amounts < 5 x 10(4) kg has indisputable positive effects on the rapidity of neutrophil engraftment, length of hospitalization and posttransplant costs, enough to make it fully justified in this situation, it is absolutely not the case when it is administered after reinfusion of CD34+38- cell amounts > 5 x 10(4) /kg. In this case, posttransplant rh-G-CSF administration could even result in a decrease in stem cells with self-renewal potential of the graft, which should still raise more concerns for its indiscriminate and costly use.
A ±50-mV Linear-Input-Range VCO-Based Neural-Recording Front-End With Digital Nonlinearity Correction (2016)

Closed-loop neuromodulation is an essential function in future neural implants for delivering efficient and effective therapy. However, a closed-loop system requires the neural-recording front-end to handle large stimulation artifacts-a feature not supported by most state-of-the-art designs. In this paper, we present a neural-recording front-end that has an input range of ±50 mV and can be used in closed-loop systems. The proposed front-end avoids the saturation due to stimulation artifacts by employing a voltage-controlled oscillator (VCO) to directly convert the input signal into the frequency domain. The VCO nonlinearity is corrected using area-efficient foreground polynomial correction. Implemented in a 40-nm CMOS process, the design occupies 0.135 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> with an analog power of 3 μW and a digital switching power of 4 μW. It achieves ten times higher linear input range than prior art, and 79-dB spurious-free dynamic range at peak input, with an input-referred noise of 5.2 μV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</sub> across the local-field-potential band of 1-200 Hz. With on-chip subhertz high-pass filters realized by duty-cycled resistors, the front-end also eliminates the need of off-chip dc-blocking capacitors.
p35, the Neuronal-specific Activator of Cyclin-dependent Kinase 5 (Cdk5) Is Degraded by the Ubiquitin-Proteasome Pathway (1998)

Cyclin-dependent kinase 5 (Cdk5) was originally isolated by its close homology to the human CDC2 gene, which is a key regulator of cell cycle progression. However, unlike other Cdks, the activity of Cdk5 is required in post-mitotic neurons. The neuronal-specific p35 protein, which shares no homology to cyclins, was identified by virtue of its association and activation of Cdk5. Gene targeting studies in mice have shown that the p35/Cdk5 kinase is required for the proper neuronal migration and development of the mammalian cortex. We have investigated the regulation of the p35/Cdk5 kinase. Here we show that p35, the activator of Cdk5, is a short-lived protein with a half-life (t1/2) of 20 to 30 min. Specific proteasome inhibitors such as lactacystin greatly stabilize p35 in vivo. Ubiquitination of p35 can be readily demonstrated in vitro and in vivo. Inhibition of Cdk5 activity by a specific Cdk inhibitor, roscovitine, or by overexpression of a dominant negative mutant of Cdk5 increases the stability of p35 by 2- to 3-fold. Furthermore, phosphorylation mutants of p35 also stabilize p35 2- to 3-fold. Together, these observations demonstrate that the p35/Cdk5 kinase can be subject to rapid turnover in vivo and suggest that phosphorylation of p35 upon Cdk5 kinase activation plays a autoregulatory role in p35 degradation mediated by ubiquitin-mediated proteolysis.
Percutaneous Peritoneal Lavage in Blunt Trauma Patients (1989)

We reviewed the records of 395 patients seen from January 1983 through May 1988, who after sustaining blunt thoracoabdominal trauma had diagnostic peritoneal lavage (DPL) performed percutaneously by the Seldinger wire technique of Lazarus and Nelson. The test was considered grossly positive if 10 cc of blood were aspirated from the catheter immediately after its insertion into the peritoneal cavity. Microscopic criteria for positivity included more than 100,000 RBC or 500 WBC/cc of lavage return, elevated amylase or bilirubin, or the presence of vegetable fibers or bacteria. Seventy-two (18%) of the patients were true positives and 315 (80%) were true negatives. There were four false positives (1.3%) and one false negative (0.2%), giving the test a sensitivity of 99% and a specificity of 98%. Complications occurred in three patients, for a rate of 0.8%, and included catheter insertion into a large ovarian dermoid cyst, needle perforation of the ileum, and needle perforation of the sigmoid colon. This technique of DPL can consistently be performed much more rapidly than the open method. Therefore we conclude that percutaneous DPL is as accurate as, as safe as, and quicker than open DPL for determining intra-abdominal injury in blunt trauma patients.
Isolation of a nontransmissible antibiotic resistance plasmid by transductional shortening of R factor RP1 (1975)

A plasmid segregant carrying tetracycline and carbenicillin resistance markers has been isolated from R factor RP1 by transductional shortening with phage P22. The new plasmid RP1-S2, which has a molecular weight of 23 times 10-6, has lost the transfer, phage sensitivity, and neomycin resistance functions of RP1. It combines readily with a W group plasmid, R388, to form a transmissible carbenicillin and trimethoprim resistance plasmid, RWP1.
Infected Aneurysm Complicated with AV Fistula and Thrombosis of the Iliac Veins and Inferior Vena Cava: A Case Demonstrated with Computed Tomography (2009)

Infected aneurysm of the abdominal artery has been found occasionally, but being accompanied with arteriovenous fistula detected by CT angiography has rarely been reported. A preoperative clinical diagnosis of infected aneurysm and arteriovenous fistula is difficult. We report a case of infected aneurysm of right common iliac artery, with the complication of arteriovenous fistula, causing thrombosis of the bilateral iliac veins and inferior vena cava. This case showed the periarterial abscess extension with partial thrombosis of iliac veins and inferior vena cava, which was not mentioned before in the literature. A contrastenhanced 64-row multiple detector CT scan with three-dimensional CT angiography is an effective, non-invasive method to detect the presence of aneurysm and its associated complications.
Gab1 Acts as an Adapter Molecule Linking the Cytokine Receptor gp130 to ERK Mitogen-Activated Protein Kinase (1998)

Gab1 has structural similarities with Drosophila DOS (daughter of sevenless), which is a substrate of the protein tyrosine phosphatase Corkscrew. Both Gab1 and DOS have a pleckstrin homology domain and tyrosine residues, potential binding sites for various SH2 domain-containing adapter molecules when they are phosphorylated. We found that Gab1 was tyrosine phosphorylated in response to various cytokines, such as interleukin-6 (IL-6), IL-3, alpha interferon (IFN-alpha), and IFN-gamma. Upon the stimulation of IL-6 or IL-3, Gab1 was found to form a complex with phosphatidylinositol (PI)-3 kinase and SHP-2, a homolog of Corkscrew. Mutational analysis of gp130, the common subunit of IL-6 family cytokine receptors, revealed that neither tyrosine residues of gp130 nor its carboxy terminus was required for tyrosine phosphorylation of Gab1. Expression of Gab1 enhanced gp130-dependent mitogen-activated protein (MAP) kinase ERK2 activation. A mutation of tyrosine 759, the SHP-2 binding site of gp130, abrogated the interactions of Gab1 with SHP-2 and PI-3 kinase as well as ERK2 activation. Furthermore, ERK2 activation was inhibited by a dominant negative p85 PI-3 kinase, wortmannin, or a dominant negative Ras. These observations suggest that Gab1 acts as an adapter molecule in transmitting signals to ERK MAP kinase for the cytokine receptor gp130 and that SHP-2, PI-3 kinase, and Ras are involved in Gab1-mediated ERK activation.
MicroRNAs and Hematopoietic Differentiation (2006)

The discovery of microRNAS (miRNAs) and of their mechanism of action has provided some very new clues on how gene expression is regulated. These studies established new concepts on how posttranscriptional control can fine-tune gene expression during differentiation and allowed the identification of new regulatory circuitries as well as factors involved therein. Because of the wealth of information available about the transcriptional and cellular networks involved in hematopoietic differentiation, the hematopoietic system is ideal for studying cell lineage specification. An interesting interplay between miRNAs and lineage-specific transcriptional factors has been found, and this can help us to understand how terminal differentiation is accomplished.
Optimal Electromagnetic Measurements (2001)

We consider the problem of obtaining information about an inaccessible half-space from electromagnetic measurements made in the accessible half-space. If the measurements are of limited precision, some scatterers will be undetectable because their scattered fields are below the precision of the measuring instrument. How can we make optimal measurements? In other words, what incident fields should we apply that will result in the biggest measurements? There are many ways to formulate this question, depending on the measuring instruments. In this paper we consider a formulation involving wave-splitting in the accessible half-space: what downgoing wave will result in an upgoing wave of greatest energy? This formulation is most natural for far-field problems. A closely related question arises in the case when we have a guess about the configuration of the inaccessible half-space. What measurements should we make to determine whether our guess is accurate? In this case we compare the scattered field to the field computed from the guessed configuration. Again we look for the incident field that results in the greatest energy difference. We show that the optimal incident field can be found by an iterative process involving time reversal "mirrors". For band-limited incident fields and compactly supported scatterers, this iterative process converges to a sum of time-harmonic fields.
Through-wall radar image reconstruction based on time-domain transient signals in the presence of noise (2005)

Through-wall radar imaging has become a keen research topic in recent years. This is due to the emphasis on homeland security, which involves many key areas such as gathering intelligence, concealed weapons detection and domestic counter-terrorism. Other applications of through-wall radar imaging include urban warfare, hostage rescue scenarios as well as search and rescue operations. This paper investigates the reconstruction of the position of objects behind walls based on the time-domain transient signals generated from a simulation program. An electromagnetic wave simulation program, using the finite difference time domain (FDTD) (1) method was used to model the transient signals as they pass through walls and interact with objects of different materials. The reflected signal was then recorded by receivers at various positions behind the wall. The difference in position between the receivers results in varying time-delays in the received signals. As a result, when the received signals are combined to form an image of the objects on the other side of the wall, the position and shape of the objects are inaccurate, resulting from the different time-delays of the radar returns. Migration techniques such as normal move-out (NMO) are used to compensate and reconstruct a more accurate shape of the objects. Time-delay correction applied to the signals is dependent on the ability to detect the presence of the transmitted pulse. This problem becomes increasingly difficult in the presence of noise. Pre-processing techniques such as low-pass filtering and Wiener filtering were applied to improve the signal detection. Keywords Finite-Difference Time-Domain (FDTD), Normal Move-out (NMO), Through-Wall Radar Imaging.
An exon skipping-associated nonsense mutation in the dystrophin gene uncovers a complex interplay between multiple antagonistic splicing elements (2006)

A nonsense mutation c.4250T>A (p.Leu1417X) in the dystrophin gene of a patient with an intermediate phenotype of muscular dystrophy induces partial in-frame skipping of exon 31. On the basis of UV cross-linking assays and pull-down analysis, we present evidence that the skipping of this exon is because of the creation of an exonic splicing silencer, which acts as a highly specific binding site (UAGACA) for a known repressor protein, hnRNP A1. Recombinant hnRNP A1 represses exon inclusion both in vitro and in vivo upon transient transfection of C2C12 cells with Duchenne muscular dystrophy (DMD) minigenes carrying the c.4250T>A mutation. Furthermore, we identified a downstream splicing enhancer in the central region of exon 31. This region functions as a Tra2beta-dependent exonic splicing enhancer (ESE) in vitro when inserted into a heterologous splicing reporter, and deletion of the ESE showed that incorporation of exon 31 depends on the Tra2beta-dependent enhancer both in the wild-type and mutant context. We conclude that dystrophin exon 31 contains juxtaposed sequence motifs that collaborate to regulate exon usage. This is the first elucidation of the molecular mechanism leading to exon skipping in the dystrophin gene and allowing the occurrence of a milder phenotype than the expected DMD phenotype. The knowledge of which cis-acting sequence within an exon is important for its definition will be essential for the alternative gene therapy approaches based on modulation of splicing to bypass DMD-causing mutations in the endogenous dystrophin gene.
At (2017)

O artigo pretende refletir e aproximar a visão de educação e arte encontrada no texto das Bases Nacionais de Componentes Curriculares - BNCC e associá-la Ã retirada da área de artes como conteúdo obrigatório do currículo do ensino médio. Para isso, apresenta o parecer sobre a primeira versão da BNCC pensado para auxiliar a equipe encarregada da escrita da parte das Artes, especificamente, Teatro. O texto oferece um roteiro de análise do documento oficial, e, por uma possibilidade interpretativa, intenta explicitar as filiações conceituais ali sutilmente presentes.Por fim, apresenta a conclusão de que a retirada das artes no currículo obrigatório do ensino médio imposta pela reforma do ensino básico em curso, já poderia ser prevista nas entrelinhas de tal documento.
Management of the Morbidly Adherent Placenta (2019)

Morbidly adherent placenta, and the spectrum of placenta accreta, increta, percreta, are becoming more commonly encountered with higher cesarean section rates. These cases are complicated by high maternal morbidity with high rates of maternal hemorrhage. This literature review discusses management of morbidly adherent placenta, from preoperative considerations and planning, to timing of delivery, and operative considerations. Care of the patient with abnormal placentation now commonly involves a multi-disciplinary team approach. Creation of care teams dedicated to the management of morbidly adherent placenta may optimize patient care and ultimately reduce morbidity.
Stout: an adaptive interface to scalable cloud storage (2010)

Many of today’s applications are delivered as scalable, multi-tier services deployed in large data centers. These services frequently leverage shared, scale-out, key-value storage layers that can deliver low latency under light workloads, but may exhibit significant queuing delay and even dropped requests under high load. Stout is a system that helps these applications adapt to variation in storage-layer performance by treating scalable key-value storage as a shared resource requiring congestion control. Under light workloads, applications using Stout send requests to the store immediately, minimizing delay. Under heavy workloads, Stout automatically batches the application’s requests together before sending them to the store, resulting in higher throughput and preventing queuing delay. We show experimentally that Stout’s adaptation algorithm converges to an appropriate batch size for workloads that require the batch size to vary by over two orders of magnitude. Compared to a non-adaptive strategy optimized for throughput, Stout delivers over 34 × lower latency under light workloads; compared to a non-adaptive strategy optimized for latency, Stout can scale to over 3 × as many requests. 1.
Enzyme activities in urine: how should we express their excretion? A critical literature review. (1991)

Different methods and reference bases for characterizing the excretion of urinary enzymes (relation to volume, time, creatinine, specific gravity, osmolality and fractional excretion) are reviewed with regard to their advantages and disadvantages when using urinary enzyme excretion as a diagnostic tool. The problems of timed and untimed urine samples for the analysis of urinary enzyme excretion and the influence of diuresis on the quantity and composition of enzymes excreted are discussed. The use of the second morning urine as a random urine sample, and determination of the relation of enzyme activity to urinary creatinine (enzyme/creatinine ratio; enzyme/creatinine index) represent a satisfactory compromise for the characterization of urinary enzyme excretion. The calculation of enzyme excretion per unit time or other modes of expression should be used only in special cases.
Large Scale Kernel Methods for Online AUC Maximization (2017)

Learning to optimize AUC performance for classifying label imbalanced data in online scenarios has been extensively studied in recent years. Most of the existing work has attempted to address the problem directly in the original feature space, which may not suitable for non-linearly separable datasets. To solve this issue, some kernel-based learning methods are proposed for non-linearly separable datasets. However, such kernel approaches have been shown to be inefficient and failed to scale well on large scale datasets in practice. Taking this cue, in this work, we explore the use of scalable kernel-based learning techniques as surrogates to existing approaches: random Fourier features and Nyström method, for tackling the problem and bring insights to the differences between the two methods based on their online performance. In contrast to the conventional kernel-based learning methods which suffer from high computational complexity of the kernel matrix, our proposed approaches elevate this issue with linear features that approximate the kernel function/matrix. Specifically, two different surrogate kernel-based learning models are presented for addressing the online AUC maximization task: (i) the Fourier Online AUC Maximization (FOAM) algorithm that samples the basis functions from a data-independent distribution to approximate the kernel functions; and (ii) the Nyström Online AUC Maximization (NOAM) algorithm that samples a subset of instances from the training data to approximate the kernel matrix by a low rank matrix. Another novelty of the present work is the proposed mini-batch Online Gradient Descent method for model updating to control the noise and reduce the variance of gradients. We provide theoretical analyses for the two proposed algorithms. Empirical studies on commonly used large scale datasets show that the proposed algorithms outperformed existing state-of-the-art methods in terms of both AUC performance and computational efficiency.