gebhart/patrepeval huggingface dataset:
Differentiation of Embryonic Stem Cells into Oligodendrocyte Precursors (2010)

Oligodendrocytes are the myelinating cells of the central nervous system. For regenerative cell therapy in demyelinating diseases, there is significant interest in deriving a pure population of lineage-committed oligodendrocyte precursor cells (OPCs) for transplantation. OPCs are characterized by the activity of the transcription factor Olig2 and surface expression of a proteoglycan NG2. Using the GFP-Olig2 (G-Olig2) mouse embryonic stem cell (mESC) reporter line, we optimized conditions for the differentiation of mESCs into GFP+Olig2+NG2+ OPCs. In our protocol, we first describe the generation of embryoid bodies (EBs) from mESCs. Second, we describe treatment of mESC-derived EBs with small molecules: (1) retinoic acid (RA) and (2) a sonic hedgehog (Shh) agonist purmorphamine (Pur) under defined culture conditions to direct EB differentiation into the oligodendroglial lineage. By this approach, OPCs can be obtained with high efficiency (>80%) in a time period of 30 days. Cells derived from mESCs in this protocol are phenotypically similar to OPCs derived from primary tissue culture. The mESC-derived OPCs do not show the spiking property described for a subpopulation of brain OPCs in situ. To study this electrophysiological property, we describe the generation of spiking mESC-derived OPCs by ectopically expressing Na(V;)1.2 subunit. The spiking and nonspiking cells obtained from this protocol will help advance functional studies on the two subpopulations of OPCs.
New treatment strategies for ulcerative colitis (2017)

Therapeutic strategies in ulcerative colitis are evolving. A personalized and optimal use of available drugs and the integration of new drug classes are the cornerstones underpinning the new treatment paradigms. Areas covered: A structured literature search in Medline and PubMed, Cochrane meta-analyses, and abstracts of international congresses has been performed to review therapeutic approaches to ulcerative colitis. The primary therapeutic objective of therapy is to achieve clinical remission since persistence of active disease, even if mild, leads to a significant reduction in quality of life. Current treatment paradigms of ulcerative colitis are based on the use of 5-aminosalycilates, corticosteroids, thiopurines, TNF-α inhibitors and α4ß7 integrin blockers. The main determinants for drug class selection are disease extension, disease severity, and previous drug history. New drug classes that will likely become available in the foreseeable future include inhibitors of Janus kinases, modulators of sphingosine-1-phosphate receptors, SMAD-7 antisense oligonucleotides, interleukin-12/23 blockers, and fecal microbiota transplantation. Expert commentary: Increasing therapeutic options for ulcerative colitis make predictors of response highly relevant. While these are not available, judicious use of therapies, avoidance of underdosing, or persistent therapy when criteria for drug failure are met are essential.
Alanine scanning mutagenesis of CCR3 reveals that the three intracellular loops are essential for functional receptor expression (2002)

Intracellular signaling mediated by the eotaxin receptor, CCR3, has been implicated in allergic diseases involving the recruitment and activation of eosinophils. To investigate the structural requirements of the three intracellular loops (ICL) of CCR3, a panel of 15 alanine triplet mutants were generated and their effects on function assessed by assays of cell surface expression and chemotactic responsiveness. While the majority of constructs were efficiently expressed when compared with their wild-type counterpart, their abilities to migrate in response to eotaxin were relatively poor, suggesting that all three intracellular loops of CCR3 are involved to some degree in coupling to G proteins. - Another panel of 7 point mutants were then constructed to examine the DRY motif which resides in ICL2 and is highly conserved throughout the chemokine receptors identified to date. The conservative mutants D130E and R131K were well tolerated and gave chemotactic responses approaching 35 % of wild-type CCR3, but the less conserved substitutions D130A, D130N and R131L were non-functioning. Tyrosine 131 was particularly sensitive to mutation as both Y131F and Y131S mutants were poorly expressed and were chemotactically inactive. Together, this data suggest that the acidic / basic / polar nature of the DRY motif is a prerequisite for CCR3 function.
Speech Dereverberation Using Fully Convolutional Networks (2018)

Speech derverberation using a single microphone is addressed in this paper. Motivated by the recent success of the fully convolutional networks (FCN) in many image processing applications, we investigate their applicability to enhance the speech signal represented by short-time Fourier transform (STFT) images. We present two variations: a “U-Net” which is an encoder-decoder network with skip connections and a generative adversarial network (GAN) with U-Net as generator, which yields a more intuitive cost function for training. To evaluate our method we used the data from the REVERB challenge, and compared our results to other methods under the same conditions. We have found that our method outperforms the competing methods in most cases.
QGene 4.0, an extensible Java QTL-analysis platform (2008)

Software and documentation are available at http://coding.plantpath.ksu.edu/qgene. Source code is available on request.
Blind Source Separation for Convolutive Mixtures of Speech using Subband processing (2002)

SMMSP2002: the 2nd International Workshop on Spectral Methods and Multirate Signal Processing, September 2002.
Real-Time Control of Low-Polymer Fracturing Fluids (2000)

Abstract Productivity gains experienced with low-polymer-concentration fracturing fluids are real. When less polymer is injected into the formation, less polymer residue remains in the proppant pack to cause damage. The 15- to 25-lbm/Mgal polymer concentration fluids now being used have been optimized to produce viscosities similar to the 30- to 40-lbm/Mgal fracturing fluids of the previous generation. Optimization is a laborious, but straightforward process with a traditional couette-type viscometer. Selected polymer-crosslinker combinations are tested to find the highest viscosity possible for the group as a function of preconditioning shear rate, temperature range, pH, ionic strength, gel stabilizer, gel breaker, surfactant, and proppant type. As each variable is optimized, its effect on the other variables must be examined to ensure the consistency of the data. If the data are consistent, mathematical modeling can be performed. Good computer models allow the practicing engineer to determine the chemical composition of a fluid required for producing a specific viscosity at a given time and temperature. The second requirement for real-time control is knowledge of the fluid temperature in the wellbore and fracture as a function of the pumping schedule (i.e., rate, volume, distance, etc.). Computer design programs can generate a pumping schedule that is ramped between chemical and proppant stages, or at least to a much larger number than the three or four stages typically used for older-generation designs. For true real-time implementation, field-scale equipment must also be able to implement the pumping schedule seamlessly. For well productivity, only chemicals required for the specific fluid segment should be pumped, without any excess. Pumping a truly optimized fluid means that the treatment is always on the edge of its performance capabilities. This paper will document the multiple effects of fluid composition on optimized viscosity, and quantify the effects on proppant transport for treatments performed at temperatures up to 300°F.
Comparative analysis of arithmetic coding computational complexity (2004)

New hardware is making obsolete previous assumptions about the most demanding computations for arithmetic coding. The important arithmetic coding tasks include: (a) interval update and arithmetic operations; (b) carry propagation and bit moves; (c) interval renormalization; (d) interval search for decoding; (e) probability estimation (source modeling); (f) support for nonbinary symbol alphabets. In this paper, the performance of binary arithmetic coding implemented with 16, 32 bit integer and 48 bit floating-point arithmetic is benchmarked. Results show that significantly faster adaptation, with small coding loss, can be obtained by periodic updates of the probability estimation.
Analysis and control of PV inverters operating in VAR mode at night (2011)

PV inverters are an important element of the future smart grids. Not only they contribute to the active power generation as distributed generators (DGs), but also they can help grid voltage/frequency stability by generating VAR. Although the number of PV installations is rapidly growing, the effective utilization of PV inverters remains low. As even if inverters are to operate in VAR mode during night hours, they still need some active power to compensate for their internal losses, regulate the DC bus and provide the desired level of reactive power. This paper will provide a detailed analysis of PV inverters' operation in VAR compensation mode when active power is not available. A new control scheme is proposed that enables inverter to absorb little active power from grid, regulate its DC bus voltage within limits, and inject the desired level of reactive power. Simulation and experimental results are provided to validate the analysis.
Suppressor Cells and Immunoregulation (1984)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Protoplast Fusion of <i>Trichoderma reesei</i> , Using Immature Conidia (1984)

Protoplast fusion of strains derived from Trichoderma reesei QM9414 and QM9136 and the segregation of the resulting fusants were studied. Combinations of protoplasts prepared from young conidia with double amino acid requirements, one of which was a common requirement and the other uncommon, were fused in the presence of polyethylene glycol 6000. Fusants were selected as regenerant colonies requiring only the commonly deficient amino acid. The frequency of fusion was 0.9 x 10 to 4.0 x 10 for the starting conidia and 3.0 x 10 to 4.9 x 10 for the regenerated protoplasts, which was significantly higher than the expected reversion frequencies by mutation. Conidia generated on the fusant colonies showed diverse phenotypes, i.e., parental types (40 to 80%) and nonparental types (20 to 60%). Colonies developed from single conidia of the nonparental phenotype contained special spots called "knobs" that have a higher density of mycelia. The phenotype of the knobs was again varied among prototrophs, parental types, and recombinant types; and their traits were inherited stably. The phenotype of the mycelia in the nonknob part was essentially the same as that of the original conidia and again formed knobs in colonies upon transfer of a piece of mycelia to a fresh medium. The conidial DNA content of the knob clone was almost the same as that of the parents, but that of the fusants was 1.2 to 2.0 times higher than that of the parents. From these results, we conclude that knobs are the segregants from the fusants. One knob clone showed twice the carboxymethyl cellulose hydrolyzing activity of the parents, suggesting the possibility of breeding T. reesei cells by the protoplast fusion technique.
Detection of caseinophosphopeptides in the distal ileostomy fluid of human subjects (2003)

Caseinophosphopeptides (CPP) were detected for the first time in ileostomy fluid, collected at 2 h intervals for 10 h post milk and CPP ingestion, from human volunteers with an ileostomy. The level of CPP present in ileostomy fluid obtained from milk-fed volunteers was markedly higher than that from volunteers fed with selected CPP preparations. The findings are based on HPLC analysis in combination with peptide-bound P determination, thin-layer electrophoresis and amino acid analysis, together with ELISA studies using polyclonal antibodies raised against a set of CPP to detect immunoreactive CPP in ileostomy fluid. These procedures allowed the detection of nm concentrations of CPP. CPP, which can be released during intestinal digestion, may function as bioactive constituents and carriers for different minerals, especially Ca, and may be used as ingredients in functional foods or pharmaceutical preparations.
Recent Developments of Molecular Chemistry for Sol–Gel Processes (1996)

Abstract This review focuses on some aspects of the chemistry involved in the preparation of oxides by sol–gel methods. This field is opening interesting possibilities for molecular chemistry and among those presented herein are: (1) the use of precursors containing functional groups for the preparation of solids with specific chemical reactivity; (2) the non‐hydrolytic gelation (NHG) route, a new general method for the synthesis of oxides that allows the use of oxygen donors (ethers, alcohols, alkoxides) other than water; the mechanism is based on oxygen–carbon bond cleavage; (3) organic–inorganic hybrid solids containing covalent bonds for which the chemical reactivity is used to demonstrate the presence of substructure in the globally amorphous solid; the substructure greatly depends on the geometry of the organic moiety.
PERK eIF2 alpha kinase is required to regulate the viability of the exocrine pancreas in mice (2007)

We conclude that PERK modulates secretory capacity of the exocrine pancreas by regulating cell viability of acinar cells.
Requirements for improved vaccines against foot-and-mouth disease epidemics (2013)

Inactivated foot-and-mouth disease (FMD) vaccines are currently used worldwide. With the emergence of various FMD virus serotypes and subtypes, vaccines must become more suitable for field-based uses under the current circumstances in terms of the fast and proper selection of vaccine strains, an extended vaccine development period for new viruses, protecting against the risk of virus leakage during vaccine manufacture, counteracting the delayed onset of immune response, counteracting shorter durations of immunity, and the accurate serological differentiation of infected and vaccinated animals and multiple vaccination. The quality of vaccines should then be improved to effectively control FMD outbreaks and minimize the problems that can arise among livestock after vaccinations. Vaccine improvement should be based on using attenuated virus strains with high levels of safety. Moreover, when vaccines are urgently required for newly spread field strains, the seed viruses for new vaccines should be developed for only a short period. Improved vaccines should offer superior immunization to all susceptible animals including cattle and swine. In addition, they should have highly protective effects without persistent infection. In this way, if vaccines are developed using new methods such as reverse genetics or vector vaccine technology, in which live viruses can be easily made by replacing specific protective antigens, even a single vaccination is likely to generate highly protective effects with an extended duration of immunity, and the safety and stability of the vaccines will be assured. We therefore reviewed the current FMD vaccines and their adjuvants, and evaluated if they provide superior immunization to all susceptible animals including cattle and swine.
Croup and Pneumonia in Human Infants Associated with a New Strain of Respiratory Syncytial Virus (1979)

Vivian Ziherl discusses her curatorial platform Frontier Imaginaries on the occasion of TOXIC ASSETS: Frontier Imaginaries Ed.No3 at e-flux, Columbia University, and UnionDocs in October 2017. In conversation with journal editor Brian Kuan Wood.\nRead Vivian Ziherl&#8217;s essay &#8220;The Fourfold Articulation&#8221; in e-flux journal #81, April 2018.\n
Dual Role of Vascular Endothelial Growth Factor in Hepatic Ischemia-Reperfusion Injury (2005)

We demonstrate a dual role of VEGF in hepatic warm I/R injury. Although endogenous VEGF is expressed and functional to initiate hepatic I/R injury, exogenous rhVEGF has a beneficial effect on the ischemic liver. These data may provide new insights into the role of VEGF as well as pathophysiology of hepatic I/R injury.
Simulation of Workflow and Threat Characteristics for Cyber Security Incident Response Teams (2014)

Within large organizations, the defense of cyber assets generally involves the use of various mechanisms, such as intrusion detection systems, to alert cyber security personnel to suspicious network activity. Resulting alerts are reviewed by the organization’s cyber security personnel to investigate and assess the threat and initiate appropriate actions to defend the organization’s network assets. While automated software routines are essential to cope with the massive volumes of data transmitted across data networks, the ultimate success of an organization’s efforts to resist adversarial attacks upon their cyber assets relies on the effectiveness of individuals and teams. This paper reports research to understand the factors that impact the effectiveness of Cyber Security Incidence Response Teams (CSIRTs). Specifically, a simulation is described that captures the workflow within a CSIRT. The simulation is then demonstrated in a study comparing the differential response time to threats that vary with respect to key characteristics (attack trajectory, targeted asset and perpetrator). It is shown that the results of the simulation correlate with data from the actual incident response times of a professional CSIRT.
MDMA-assisted therapy for severe PTSD: a randomized, double-blind, placebo-controlled phase 3 study (2021)

Post-traumatic stress disorder (PTSD) presents a major public health problem for which currently available treatments are modestly effective. We report the findings of a randomized, double-blind, placebo-controlled, multi-site phase 3 clinical trial (NCT03537014) to test the efficacy and safety of 3,4-methylenedioxymethamphetamine (MDMA)-assisted therapy for the treatment of patients with severe PTSD, including those with common comorbidities such as dissociation, depression, a history of alcohol and substance use disorders, and childhood trauma. After psychiatric medication washout, participants (n = 90) were randomized 1:1 to receive manualized therapy with MDMA or with placebo, combined with three preparatory and nine integrative therapy sessions. PTSD symptoms, measured with the Clinician-Administered PTSD Scale for DSM-5 (CAPS-5, the primary endpoint), and functional impairment, measured with the Sheehan Disability Scale (SDS, the secondary endpoint) were assessed at baseline and at 2 months after the last experimental session. Adverse events and suicidality were tracked throughout the study. MDMA was found to induce significant and robust attenuation in CAPS-5 score compared with placebo (P < 0.0001, d = 0.91) and to significantly decrease the SDS total score (P = 0.0116, d = 0.43). The mean change in CAPS-5 scores in participants completing treatment was -24.4 (s.d. 11.6) in the MDMA group and -13.9 (s.d. 11.5) in the placebo group. MDMA did not induce adverse events of abuse potential, suicidality or QT prolongation. These data indicate that, compared with manualized therapy with inactive placebo, MDMA-assisted therapy is highly efficacious in individuals with severe PTSD, and treatment is safe and well-tolerated, even in those with comorbidities. We conclude that MDMA-assisted therapy represents a potential breakthrough treatment that merits expedited clinical evaluation.
Imbibition of Picoliter Water Droplets on Coated Inkjet Papers (2010)

When an impinged inkjet droplet is impacting a paper substrate, it evaporates to the air and penetrates into the paper. The imbibition dynamics are strongly dependant on the pore structure on the surface and inside the substrate. In this work picoliter (pL) water droplets were impinged onto two commercially available matte and gloss coated paper sample. The imbibition process was recorded and analyzed using a high speed imaging system. Calculations of the volume change were done by considering that the droplets are shaped as hemispherical caps. The total drying time of water droplets of about 60 pL is 10-15 ms on the gloss coated paper, and d 30-150 ms on n the matte coated paper. In addition, the two samples show different regimes in the imbibition process caused by the different porous structures present in the samples.
The effect of microdebriders on tissue for histological diagnosis (1997)

Microdebriders are an innovation in endonasal surgery which enable accurate and precise removal of tissue without damaging the surrounding mucosa. Concern has been expressed, however, that the instrument may render excised tissue unsuitable for histological diagnosis. This problem is further compounded by the fact that the Hummer (Stryker UK Ltd) microdebrider does not incorporate a mechanism for collecting specimens at the time of removal. Twenty-one patients with sinonasal polyposis underwent endoscopic sinus surgery using the microdebrider. Specimens were collected at the time of surgery via an in-line specimen trap. Simultaneous conventional biopsies of adjacent tissue were taken for comparison. The tissue was fixed in formalin then routinely processed to paraffin wax prior to staining with haematoxylin and eosin (H&E). A histological diagnosis was made in all 21 patients. A single unsuspected transitional cell papilloma was found. The remaining 20 specimens consisted of inflammatory nasal polypi. In two non-caseating granulomas were identified. Traumatic artefact was limited to the respiratory epithelium. The sub-epithelial tissue was unaffected and metaplastic epithelium appeared intact. The use of microdebriders does not preclude the submission of tissue for histological analysis. Tissue obtained has limited artefact and is suitable for pathological diagnosis.
Structure and expression of the murine N-myc gene. (1986)

We have demonstrated that the entire murine N-myc gene and the sequences necessary for its expression in human neuroblastoma cells are contained within a 7.4-kilobase murine genomic clone. The complete nucleotide sequence of this gene reveals a number of striking similarities and differences when compared to the related c-myc gene including the following: (i) each gene contains three exons of which the first encodes a long 5'-untranslated leader sequence; (ii) the coding regions of the N- and c-myc genes share regions of substantial nucleic acid homology, the putative N-myc protein shares substantial homology with the c-myc protein; (iii) as with c-myc, extensive nucleotide sequence homology exists between the untranslated regions of the human and murine N-myc gene transcripts; however, the N-myc and c-myc untranslated regions are totally divergent; (iv) the N-myc transcriptional promoter differs from that of c-myc and is more related to the promoter of the simian virus 40. We discuss these findings in the context of previously defined similarities and differences in the potential functional and regulatory aspects of these two myc-family members.