gebhart/patrepeval huggingface dataset:
Activin A Efficiently Specifies Definitive Endoderm from Human Embryonic Stem Cells Only When Phosphatidylinositol 3-Kinase Signaling Is Suppressed (2007)

Human ESCs (hESCs) respond to signals that determine their pluripotency, proliferation, survival, and differentiation status. In this report, we demonstrate that phosphatidylinositol 3-kinase (PI3K) antagonizes the ability of hESCs to differentiate in response to transforming growth factor beta family members such as Activin A and Nodal. Inhibition of PI3K signaling efficiently promotes differentiation of hESCs into mesendoderm and then definitive endoderm (DE) by allowing them to be specified by Activin/Nodal signals present in hESC cultures. Under conditions where hESCs are grown in mouse embryo fibroblast-conditioned medium under feeder-free conditions, approximately 70%-80% are converted into DE following 5 days of treatment with inhibitors of the PI3K pathway, such as LY 294002 and AKT1-II. Microarray and quantitative polymerase chain reaction-based gene expression profiling demonstrates that definitive endoderm formation under these conditions closely parallels that following specification with elevated Activin A and low fetal calf serum (FCS)/knockout serum replacement (KSR). Reduced insulin/insulin-like growth factor (IGF) signaling was found to be critical for cell fate commitment into DE. Levels of insulin/IGF present in FCS/KSR, normally used to promote self-renewal of hESCs, antagonized differentiation. In summary, we show that generation of hESC-DE requires two conditions: signaling by Activin/Nodal family members and release from inhibitory signals generated by PI3K through insulin/IGF. These findings have important implications for our understanding of hESC self-renewal and early cell fate decisions.
Analysts' utilization of historical earnings information (1991)

Abstract This study examines whether security analysts (in)efficiently utilize the information contained in past series of annual and quarterly earnings in producing earnings forecasts. To do so, it investigates whether equal‐weighted combinations of security analysts' forecasts with forecasts from statistical models based on historical earnings are superior, both in terms of being a better surrogate for the market's expectations of earnings and of accuracy, to forecasts from either one of these two sources. The empirical findings indicate that, although analysts' forecasts are superior to forecasts from statistical models, performance can be improved—both in terms of accuracy and also of being a better surrogate for market earnings expectations—by combining analysts' forecasts with forecasts from statistical models based on past quarterly earnings. Improvements in proxying for market earnings expectations were obtained even when analysts' forecasts made in June of the forecast year were used in the combinations. An implication of these findings is that investors can improve their investment decisions by using an average of the mean analysts' forecasts and the forecast produced by a time‐series model of quarterly earnings in their investment decisions.
Automated categorization in the international patent classification (2003)

A new reference collection of patent documents for training and testing automated categorization systems is established and described in detail. This collection is tailored for automating the attribution of international patent classification codes to patent applications and is made publicly available for future research work. We report the results of applying a variety of machine learning algorithms to the automated categorization of English-language patent documents. This procedure involves a complex hierarchical taxonomy, within which we classify documents into 114 classes and 451 subclasses. Several measures of categorization success are described and evaluated. We investigate how best to resolve the training problems related to the attribution of multiple classification codes to each patent document.
Completing the structural family portrait of the human EphB tyrosine kinase domains (2014)

The EphB receptors have key roles in cell morphology, adhesion, migration and invasion, and their aberrant action has been linked with the development and progression of many different tumor types. Their conflicting expression patterns in cancer tissues, combined with their high sequence and structural identity, present interesting challenges to those seeking to develop selective therapeutic molecules targeting this large receptor family. Here, we present the first structure of the EphB1 tyrosine kinase domain determined by X-ray crystallography to 2.5Å. Our comparative crystalisation analysis of the human EphB family kinases has also yielded new crystal forms of the human EphB2 and EphB4 catalytic domains. Unable to crystallize the wild-type EphB3 kinase domain, we used rational engineering (based on our new structures of EphB1, EphB2, and EphB4) to identify a single point mutation which facilitated its crystallization and structure determination to 2.2 Å. This mutation also improved the soluble recombinant yield of this kinase within Escherichia coli, and increased both its intrinsic stability and catalytic turnover, without affecting its ligand-binding profile. The partial ordering of the activation loop in the EphB3 structure alludes to a potential cis-phosphorylation mechanism for the EphB kinases. With the kinase domain structures of all four catalytically competent human EphB receptors now determined, a picture begins to emerge of possible opportunities to produce EphB isozyme-selective kinase inhibitors for mechanistic studies and therapeutic applications.
Rapid glutamatergic alterations in the neural retina induced by retinal detachment. (2000)

These results indicate that retinal detachment induces rapid, localized alterations in the glutamatergic system of the neural retina that are consistent with a massive efflux of neuronal glutamate and concomitant alterations in glutamate metabolism. An acute efflux of neuronal glutamate in detached retina could contribute to excitotoxicity and to the initiation of structural alterations and changes in gene expression; it is also consistent with reported neurochemical changes associated with longer term retinal detachment.
The developer's handbook to DB2 for common servers (1997)

From the Publisher:
Reviewed for accuracy by a team of IBM analysts and DB2 specialists,this authoritative,one-stop reference to development DB2/2 and DB2/6000 applications is the only comprehensive and up-to-date sourcebook on the latest versions of the red-hot database software that doubled its sales in the past year. Author Roger E. Sanders provides complete source code examples in this logically organized,impressively sized volume. He covers the underlying database architecture,application development fundamentals,and the latest tools for developing object-oriented DB2/2 and DB2/6000 database applications.
Intestinal secretion of immunoglobulins and antibodies to Escherichia coli in the pig. (1970)

Immunoglobulins and antibodies against Escherichia coli 0141 have been studied in porcine intestinal secretions obtained from Thiry Vella loops prepared in the mid jejunum of 4 animals. The molecular size of the secreted immunoglobulins were investigated by gel filtration and sucrose density gradient ultra-centrifugation. Intestinal IgM was found to have 7S characteristics and intestinal IgA mainly 11S characteristics similar to secretory IgA isolated from porcine milk. Immune inhibition studies with rabbit anti-IgA-globulin serum produced complete elimination of E. coli 0141 antibodies detected by direct haemagglutination. In one animal incomplete antibody assayed by antiglobulin haemagglutination was identified in fractions associated with IgM and IgG. Immunofluorescent studies were made to correlate immunoglobulins in the small intestinal tissue with weaning.
Tumor-Specific Activation of an EGFR-Targeting Probody Enhances Therapeutic Index (2013)

Target-mediated toxicity constitutes a major limitation for the development of therapeutic antibodies. To redirect the activity of antibodies recognizing widely distributed targets to the site of disease, we have applied a prodrug strategy to create an epidermal growth factor receptor (EGFR)-directed Probody therapeutic-an antibody that remains masked against antigen binding until activated locally by proteases commonly active in the tumor microenvironment. In vitro, the masked Probody showed diminished antigen binding and cell-based activities, but when activated by appropriate proteases, it regained full activity compared to the parental anti-EGFR antibody cetuximab. In vivo, the Probody was largely inert in the systemic circulation of mice, but was activated within tumor tissue and showed antitumor efficacy that was similar to that of cetuximab. The Probody demonstrated markedly improved safety and increased half-life in nonhuman primates, enabling it to be dosed safely at much higher levels than cetuximab. In addition, we found that both Probody-responsive xenograft tumors and primary tumor samples from patients were capable of activating the Probody ex vivo. Probodies may therefore improve the safety profile of therapeutic antibodies without compromising efficacy of the parental antibody and may enable the wider use of empowered antibody formats such as antibody-drug conjugates and bispecifics.
Total synthesis of calicheamicinone: a solution to the problem of the elusive urethane (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of calicheamicinone: a solution to the problem of the elusive urethaneMaria Paz Cabal, Robert S. Coleman, and Samuel J. DanishefskyCite this: J. Am. Chem. Soc. 1990, 112, 8, 3253–3255Publication Date (Print):April 1, 1990Publication History Published online1 May 2002Published inissue 1 April 1990https://pubs.acs.org/doi/10.1021/ja00164a079https://doi.org/10.1021/ja00164a079research-articleACS PublicationsRequest reuse permissionsArticle Views1086Altmetric-Citations71LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
PTEN expression is consistent in colorectal cancer primaries and metastases and associates with patient survival (2013)

Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) negatively regulates the phosphoinositide-3-kinase (PI3K) signaling pathway. In colorectal cancer (CRC), observed frequencies of loss of PTEN expression, concordant expression in primary tumors and metastases, and the association of PTEN status with outcome vary markedly by detection method. We determined the degree to which PTEN expression is consistent in 70 matched human CRC primaries and liver metastases using a validated immunohistochemistry assay. We found loss of PTEN expression in 12.3% of assessable CRC primaries and 10.3% of assessable liver metastases. PTEN expression (positive or negative) was concordant in 98% of matched colorectal primaries and liver metastases. Next we related PTEN status to mutations in RAS and PI3K pathway genes (KRAS, NRAS, BRAF , and PIK3CA) and to overall survival (OS). PTEN expression was not significantly associated with the presence or absence of mutations in RAS or PI3K pathway genes. The median OS of patients whose tumors did not express PTEN was 9 months, compared to 49 months for patients whose tumors did express PTEN (HR = 6.25, 95% confidence intervals (CI) (1.98, 15.42), P = 0.0017). The association of absent PTEN expression with increased risk of death remained significant in multivariate analysis (HR = 6.31, 95% CI (2.03, 17.93), P = 0.0023). In summary, PTEN expression was consistent in matched CRC primaries and in liver metastases. Therefore, future investigations of PTEN in metastatic CRC can use primary tumor tissue. In patients with liver-only metastases, loss of PTEN expression predicted poor OS.
Engineering neuronal growth cones to promote axon regeneration over inhibitory molecules (2011)

Neurons in the central nervous system (CNS) fail to regenerate axons after injuries due to the diminished intrinsic axon growth capacity of mature neurons and the hostile extrinsic environment composed of a milieu of inhibitory factors. Recent studies revealed that targeting a particular group of extracellular inhibitory factors is insufficient to trigger long-distance axon regeneration. Instead of antagonizing the growing list of impediments, tackling a common target that mediates axon growth inhibition offers an alternative strategy to promote axon regeneration. Neuronal growth cone, the machinery that derives axon extension, is the final converging target of most, if not all, growth impediments in the CNS. In this study, we aim to promote axon growth by directly targeting the growth cone. Here we report that pharmacological inhibition or genetic silencing of nonmuscle myosin II (NMII) markedly accelerates axon growth over permissive and nonpermissive substrates, including major CNS inhibitors such as chondroitin sulfate proteoglycans and myelin-associated inhibitors. We find that NMII inhibition leads to the reorganization of both actin and microtubules (MTs) in the growth cone, resulting in MT reorganization that allows rapid axon extension over inhibitory substrates. In addition to enhancing axon extension, we show that local blockade of NMII activity in axons is sufficient to trigger axons to grow across the permissive-inhibitory border. Together, our study proposes NMII and growth cone cytoskeletal components as effective targets for promoting axon regeneration.
Influenza: current threat from avian influenza (2005)

Influenza is an infectious respiratory pathogen causing annual outbreaks and infrequent pandemics, resulting in significant morbidity, mortality and burdens on the delivery of health care. The geographical spread of highly pathogenic avian influenza (HPAI) H5N1 among poultry and wild bird populations is unprecedented. Growing numbers of sporadic avian influenza infections are occurring in humans, increasing the threat of the next influenza pandemic. Vaccines are the principle means of combating influenza, and a number of studies with H5N1 vaccine candidates are underway. Antiviral agents can be used to treat influenza infection and can be taken as chemoprophylaxis during influenza outbreaks. Oseltamivir has been stockpiled as part of influenza pandemic preparedness planning; however, the emergence of drug resistance may limit its clinical use.
Renal Tubulointerstitial Changes after Internal Irradiation with α-Particle–Emitting Actinium Daughters (2005)

The effect of external gamma irradiation on the kidneys is well described. However, the mechanisms of radiation nephropathy as a consequence of targeted radionuclide therapies are poorly understood. The functional and morphologic changes were studied chronologically (from 10 to 40 wk) in mouse kidneys after injection with an actinium-225 (225Ac) nanogenerator, a molecular-sized, antibody-targeted, in vivo generator of alpha-particle-emitting elements. Renal irradiation from free, radioactive daughters of 225Ac led to time-dependent reduction in renal function manifesting as increase in blood urea nitrogen. The histopathologic changes corresponded with the decline in renal function. Glomerular, tubular, and endothelial cell nuclear pleomorphism and focal tubular cell injury, lysis, and karyorrhexis were observed as early as 10 wk. Progressive thinning of the cortex as a result of widespread tubulolysis, collapsed tubules, glomerular crowding, decrease in glomerular cellularity, interstitial inflammation, and an elevated juxtaglomerular cell count were noted at 20 to 30 wk after treatment. By 35 to 40 wk, regeneration of simplified tubules with tubular atrophy and loss with focal, mild interstitial fibrosis had occurred. A lower juxtaglomerular cell count with focal cytoplasmic vacuolization, suggesting increased degranulation, was also observed in this period. A focal increase in tubular and interstitial cell TGF-beta1 expression starting at 20 wk, peaking at 25 wk, and later declining in intensity with mild increase in the extracellular matrix deposition was noticed. These findings suggest that internally delivered alpha-particle irradiation-induced loss of tubular epithelial cells triggers a chain of adaptive changes that result in progressive renal parenchymal damage accompanied by a loss of renal function. These findings are dissimilar to those seen after gamma or beta irradiation of kidneys.
Video Forensics in Temporal Domain using Machine Learning Techniques (2013)

In defence and military scenarios, Un manned Aerial Vehicle (UA V) is used for surveillance missions. UA V's transmit live v ideo to the base station. Temporal attacks may be carried out by the intruder during video transmission. These temporal attacks can be used to add/delete objects, individuals, etc. in the live transmission feed. This can cause the video informat ion to misrepresent facts of the UA V transmission. Hence, it is needed to identify the fake video fro m the real ones. Co mpression techniques like MPEG, H.263, etc. are popularly used to compress videos. Attacker can either add/delete frames fro m v ideos to introduce/remove objects, individuals etc. from video. In order to perform attack on the video, the attacker has to uncompress the video and perform addition/deletion of frames. Once the attack is done, the attacker needs to recompress the frames to a video. Wang and Farid et. al. [1] proposed a method based on double compression technique to detect temporal fingerprints left in the video caused due to frame addit ion/deletion. Based on double MPEG compression, here we propose a video forensic technique using machine learning techniques to detect video forgery. In order to generate a unique feature vector to identify forged video, we analysed the effect of attacks on Prediction Error Sequence (PES) in various domains like Discrete Cosine Transform (DCT), Discrete Fourier Transform (DFT), Discrete Wavelet Transform (DWT) domain etc. A new PES feature is defined and extracted fro m DWT domain, which is proven robust training parameter for both Support Vector Machine (SVM ) and ensemble based classifier. The t rained SVM was tested for unknown videos to find video forgery. Experimental results show that our proposed video forensic is robust and efficient in detecting video forgery without any human intervention. Further the proposed system is simp ler in design and imp lementation and also scalable for testing large nu mber of v ideos.
Chemoenzymatic Synthesis with Distinct Pasteurella Heparosan Synthases MONODISPERSEPOLYMERSANDUNNATURALSTRUCTURES (2007)

Heparosan (-GlcUA-1,4-GlcNAc-1,4-)n is a member of the glycosaminoglycan polysaccharide family found in the capsule of certain pathogenic bacteria as well as the precursor for the vertebrate polymers, heparin and heparan sulfate. The two heparosan synthases from the Gram-negative bacteria Pasteurella multocida, PmHS1 and PmHS2, were efficiently expressed and purified using maltose-binding protein fusion constructs. These relatively homologous synthases displayed distinct catalytic characteristics. PmHS1, but not PmHS2, was able to produce large molecular mass (100 – 800 kDa) monodisperse polymers in synchronized, stoichiometrically controlled reactions in vitro. PmHS2, but not PmHS1, was able to utilize many unnatural UDP-sugar analogs (including substrates with acetamido-containing uronic acids or longer acyl chain hexosamine derivatives) in vitro. Overall these findings reveal potential differences in the active sites of these two Pasteurella enzymes. In the future, these catalysts should allow the creation of a variety of heparosan and heparinoids with utility for medical applications.
Antisense oligonucleotide treatments for psoriasis (2004)

Antisense oligonucleotides are emerging as an exciting therapeutic strategy for treating skin diseases such as psoriasis. Potential antisense targets are proteins upregulated in psoriatic skin, in particular those associated with inflammation (intercellular adhesion molecule [ICAM]-1, IL-2 and -8), proliferation (insulin-like growth factor type I receptor [IGF-IR], epidermal growth factor) and hyperangiogenesis (vascular endothelial growth factor [VEGF]). Whereas topical application and subsequent penetration of large oligonucleotides into normal skin is problematic, the impaired barrier function of psoriatic lesions permits the uptake of antisense drugs. Studies to date indicate that topically applied antisense molecules can be delivered to target cells in the epidermis and dermis of psoriatic skin. Antisense-mediated suppression of target mRNA and protein has been demonstrated in models of human skin grafted to immunosuppressed mice and in hairless mouse models of skin inflammation. In a xenograft model of human psoriasis, treatment with repeated intradermal injections of IGF-IR antisense caused a normalisation of the epidermal hyperproliferation. This class of drug, therefore, holds much potential for the successful treatment of psoriasis in the clinical setting.
Antibody-dependent antitumor cytotoxicity by human monocytes cultured with recombinant macrophage colony-stimulating factor. Induction of efficient antibody-mediated antitumor cytotoxicity not detected by isotope release assays. (1989)

Macrophage colony-stimulating factor (M-CSF) is known to stimulate proliferation of monocyte/macrophage progenitors and enhance in vitro antitumor cytotoxicity by murine macrophages. In this paper we have shown that recombinant human M-CSF causes human peripheral blood monocytes to differentiate in culture into metabolically active macrophage-like cells. These cells mediate very efficient antibody-dependent cellular cytotoxicity (ADCC) against human melanoma and neuroblastoma cell lines in the presence of two murine IgG3 mAbs (3F8 and R24). They also mediate antibody-independent cytotoxicity (or cytostasis) to a lesser extent. Human serum had an inconsistent effect on ADCC, but often induced similar high levels of ADCC. Cytotoxicity was measured using a novel ELISA to detect surviving tumor cells after ADCC. Two conventional isotope-release assays (51Cr and [3H]TdR) underestimated or entirely failed to detect ADCC by M-CSF-activated monocytes. Optimal activation occurred with 100-300 U/ml of M-CSF, and required 9-11 d for completion. Most of the M-CSF cultured monocytes expressed the low-affinity Fc receptor (CD16). ADCC by cells of the monocyte/macrophage lineage using murine IgG3 mAbs may have significance for the immunotherapy of human malignancies.