gebhart/patrepeval huggingface dataset:
Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions (2016)

The increasing diagnostic use of gene sequencing has led to an expanding dataset of novel variants that lie within consensus splice junctions. The challenge for diagnostic laboratories is the evaluation of these variants in order to determine if they affect splicing or are merely benign. A common evaluation strategy is to use in silico analysis, and it is here that a number of programmes are available online; however, currently, there are no consensus guidelines on the selection of programmes or protocols to interpret the prediction results. Using a collection of 222 pathogenic mutations and 50 benign polymorphisms, we evaluated the sensitivity and specificity of four in silico programmes in predicting the effect of each variant on splicing. The programmes comprised Human Splice Finder (HSF), Max Entropy Scan (MES), NNSplice, and ASSP. The MES and ASSP programmes gave the highest performance based on Receiver Operator Curve analysis, with an optimal cut-off of score reduction of 10%. The study also showed that the sensitivity of prediction is affected by the level of conservation of individual positions, with in silico predictions for variants at positions -4 and +7 within consensus splice sites being largely uninformative.
Dynamic expression of Dab2 in the mouse embryonic central nervous system (2008)

This is the first study to demonstrate the dynamic spatiotemporal expression of Dab2 protein within the CNS during development.
Fludarabine Compared with Chlorambucil as Primary Therapy for Chronic Lymphocytic Leukemia (2000)

When used as the initial treatment for chronic lymphocytic leukemia, fludarabine yields higher response rates and a longer duration of remission and progression-free survival than chlorambucil.
A review of murine models of latent tuberculosis infection (2011)

The mechanisms of latency and the causes of reactivation of Mycobacterium tuberculosis remain poorly understood; an important reason for this gap in knowledge is the absence of a standardized animal model of latent tuberculosis infection (LTBI). A complete LTBI model should incorporate 2 aspects of LTBI: a persistent infection model with a low bacterial load and a latent infection model that is modified from the Cornell model. Many parameters must be carefully considered to establish an LTBI model, including the inoculating dose, the route of infection, the time interval between infection and the initiation of antibiotic therapy, and the genetic background of the host animal. The responsiveness of this mouse model of LTBI can be assessed through the integrated use of indices, including Karnofsky performance status, bacterial load in spleen and lungs, induced levels of interferon-gamma and tumour necrosis factor-alpha, expression of interleukin (IL)-10 and IL-4 in tissues, specific antigen load in organs, time required for hormone-induced TB relapse, expression level of dormancy genes, and CD4 T-cell count.
Activation of the Sphingosine Kinase–Signaling Pathway by High Glucose Mediates the Proinflammatory Phenotype of Endothelial Cells (2005)

Vascular endothelial cells are key targets for hyperglycemic damage that facilitates vascular inflammation and the vasculopathy associated with diabetes mellitus. However, the mechanisms underlying this damage remain undefined. We now demonstrate that hyperglycemia induces activation of sphingosine kinase (SphK), which represents a novel signaling pathway that mediates endothelial damage under ambient high glucose conditions. SphK activity was significantly increased in aorta and heart of streptozotocin-induced diabetic rats. Interestingly, this increase in SphK activity was prevented by insulin treatment, which achieved euglycemia in the diabetic animals. Hyperglycemia-induced increase in SphK activity was also evident in endothelial cells that received long-term exposure to high glucose (22 mmol/L). Studies using a small interfering RNA strategy demonstrated that endogenous SphK1, but not SphK2, is the major isoenzyme that was activated by high glucose. In addition, an increase in SphK1 phosphorylation was detected in a protein kinase C- and extracellular signal-regulated kinase 1/2-dependent manner, which accounts for the high glucose-induced increases in SphK activity. Importantly, inhibition of SphK1 by either a chemical inhibitor (N',N'-dimethylsphingosine) or expression of a dominant-negative mutant of SphK1 (SphK(G82D)), or SphK1-specific small interfering RNA, strongly protected endothelial cells against high glucose-induced damage, as characterized by an attenuation in the expression of proinflammatory adhesion molecules, adhesion of leukocytes to endothelial cells, and nuclear factor kappaB activation. Thus, interventions that target the SphK-signaling pathway may have the potential to prevent vascular lesions under hyperglycemic conditions.
Adoptive immunotherapy with donor lymphocyte transfusions (1997)

Adoptive immunotherapy denotes the transfer of immunocompetent cells for the treatment of leukemia, cancer, or viral disease. It has regained much interest through the success of treating recurrent leukemia after allogeneic bone marrow transplantation with the transfusion of donor lymphocytes. Chimerism and transplantation tolerance toward the donor offer the possibility of adoptive immunotherapy using donor lymphocytes. In animal studies, donor lymphocytes could be transfused into the chimeric animal, if the transfusion was delayed after marrow transplantation. Transfused lymphocytes exhibit a graft-versus-leukemia effect and increase chimerism. Immunity could be transferred and immune reactivity toward new antigens improved. In human patients transfusion of donor lymphocytes was studied in leukemia recurring after marrow transplantation. It was very effective in the treatment of chronic myelogenous leukemia recurring after marrow transplantation. It was also effective in some patients with acute myeloid leukemia, myelodysplastic syndrome and myeloma; in acute lymphoblastic leukemia and lymphoma responses were rare. Responses in solid tumors as breast cancer have been described. Major complications are graft-versus-host disease and myelosuppression. Myelosuppression could be compensated by the transfusion of marrow. Graft-versus-host disease can be modified by the depletion of CD8-positive T cells from the lymphocyte concentrate or by transfusing very low numbers of cells and increasing doses in a stepwise fashion. The role of concomitant treatment with cytokines and activation of T cells by dendritic cells and vaccination remains to be defined.
NGEP, a gene encoding a membrane protein detected only in prostate cancer and normal prostate (2004)

We identified a gene (NGEP) that is expressed only in prostate cancer and normal prostate. The two NGEP transcripts are 0.9 kb and 3.5 kb in size and are generated by a differential splicing event. The short variant (NGEP-S) is derived from four exons and encodes a 20-kDa intracellular protein. The long form (NGEP-L) is derived from 18 exons and encodes a 95-kDa protein that is predicted to contain seven-membrane-spanning regions. In situ hybridization shows that NGEP mRNA is localized in epithelial cells of normal prostate and prostate cancers. Immunocytochemical analysis of cells transfected with NGEP cDNAs containing a Myc epitope tag at the carboxyl terminus shows that the protein encoded by the short transcript is localized in the cytoplasm, whereas the protein encoded by the long transcript is present on the plasma membrane. Because of its selective expression in prostate cancer and its presence on the cell surface, NGEP-L is a promising target for the antibody-based therapies of prostate cancer.
Side‐Chain Modification and “Grafting Onto” via Olefin Cross‐Metathesis (2012)

Olefin cross-metathesis is introduced as a versatile polymer side-chain modification technique. The reaction of a poly(2-oxazoline) featuring terminal double bonds in the side chains with a variety of functional acrylates has been successfully performed in the presence of Hoveyda-Grubbs second-generation catalyst. Self-metathesis, which would lead to polymer-polymer coupling, can be avoided by using an excess of the cross-metathesis partner and a catalyst loading of 5 mol%. The results suggest that bulky acrylates reduce chain-chain coupling due to self-metathesis. Moreover, different functional groups such as alkyl chains, hydroxyl, and allyl acetate groups, as well as an oligomeric poly(ethylene glycol) and a perfluorinated alkyl chain have been grafted with quantitative conversions.
WIT3: Web Inventory of Transcribed and Translated Talks (2012)

We describe here a Web inventory named WIT 3 that offers access to a collection of transcribed and translated talks. The core of WIT 3 is the TED Talks corpus, that basically redistributes the original content published by the TED Conference website (http://www.ted.com). Since 2007, the TED Conference, based in California, has been posting all video recordings of its talks together with subtitles in English and their translations in more than 80 languages. Aside from its cultural and social relevance, this content, which is published under the Creative Commons BYNC-ND license, also represents a precious language resource for the machine translation research community, thanks to its size, variety of topics, and covered languages. This effort repurposes the original content in a way which is more convenient for machine translation researchers.
COFDM: an overview (1995)

The research and development of OFDM/COFDM for digital television broadcasting has received considerable attention and has made a great deal of progress in Europe. OFDM/COFDM has already been implemented in digital audio broadcasting and is being considered for terrestrial digital television and HDTV broadcasting. The advantages of COFDM claimed by the advocates in Europe have also caught the attention of US broadcasters and generated enthusiasm although a digital modulation technique called 8-VSB has been selected by the FCC Advisory Committee on Advanced Television Service (ACATS) for the final testing. There is considerable debate in the industry over the use of COFDM vs. VSB or QAM for terrestrial HDTV broadcasting. In this paper, the history of research and development on OFDM and COFDM is reviewed. Then, the basic principles, performance and implementation of OFDM and COFDM are examined. Analysis is given to enable the selection of key elements for meeting the constraints of the required applications. Based on the ATV channel model, performance expectation of COFDM under imperfect channel conditions and implementation issues are examined in details.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Redirecting Effector T Cells Through Their IL-2 Receptors (1999)

Fusion proteins constructed of a tumor-specific Ab joined to IL-2 (Ab-IL-2) have been used in the past to deliver cytokine directly to the site of tumor cells in vivo. These molecules mimic the activity of IL-2 and assist in activating and expanding antitumor effector cells. To enhance the cytolytic activity of CTL specific for peptide epitopes of the Her-2/neu tumor Ag presented by HLA-A*0201 molecules, a fusion protein was constructed consisting of a single chain Ab specific for Her-2/neu, linked to IL-2 (neu-Ab-IL-2). When added to a mixture of tumor cells and Her-2/neu-specific CTL, the protein was found to augment lysis of tumor cells. In addition, the hybrid molecule also promoted lysis of Her-2/neu expressing tumors by non-tumor-specific cloned T cell lines, including Th1 CD4 cells. Analysis of the mechanism of cytotoxicity revealed that the fusion protein mediates the formation of stable conjugates between T cells expressing IL-2R and tumor cells expressing Her-2/neu, resulting in lysis through the Fas-Fas ligand pathway. Lysis induction was independent of specific engagement by the TCR. When tested for its ability to enhance tumor cell eradication by Her-2/neu-specific CD8+ T cells in an adoptive transfer model in SCID mice, neu-Ab-IL-2 facilitated the elimination of tumor cells in vivo. Surprisingly, the combination of non-tumor-specific CD8+ T cells and fusion protein also induced a significant delay of tumor growth. This represents a novel approach for redirecting non-tumor-specific T cells to eliminate tumors.
Immediate Hormonal Therapy Compared with Observation after Radical Prostatectomy and Pelvic Lymphadenectomy in Men with Node-Positive Prostate Cancer (1999)

Immediate antiandrogen therapy after radical prostatectomy and pelvic lymphadenectomy improves survival and reduces the risk of recurrence in patients with node-positive prostate cancer.
Boron Removal via Formation of Magnesium Silicate Solids during Precipitative Softening (2007)

Precipitative softening is an option to remove silicon and boron from natural waters. Silicon was removed from hard waters by precipitative softening when the molar ratio of Mg:Si was less than 6:1 by the formation of an amorphous magnesium silicate. This solid had an apparent solubility product constant of 10−25.66 and was stoichiometrically similar to the mineral forsterite, Mg2SiO4 . Boron removal was consistent with sorption to this amorphous magnesium silicate and could be roughly described by a Freundlich isotherm: Bsorb∕Mg2SiO4(s)=21×Bsol0.51 .
Targeted prodrug treatment of HER‐2‐positive breast tumor cells using trastuzumab and paclitaxel linked by A‐Z‐CINNTM Linker (2003)

Targeting drugs for delivery and release has the potential to increase the efficacy of treatment. A bifunctional linker, A-Z-CINN Linker was used to create a targeted prodrug, A-Z-CINN 310. A-Z-CINN Linker links to a potent chemotherapeutic agent, paclitaxel, via an energy-reversible ester bond and also binds a targeting agent, the monoclonal antibody trastuzumab (Herceptin). This study demonstrates the effectiveness of a single-treatment use of A-Z-CINN 310 in decreasing tumor volume and tumor cell density of human HER-2-positive BT-474 mammary tumor cells implanted in scid mice, compared to treatment with simultaneously administered trastuzumab and paclitaxel and with saline control. After treatment with A-Z-CINN 310, some mice received light exposure at 6 h for 5 min adjacent to the tumor to cause light-accelerated release of paclitaxel. Changes in tumor volume were measured for 28 days following treatment; changes in histology were measured at 31 days. Animals treated with A-Z-CINN 310, then light, showed dose-dependent decreases in tumor volume and tumor cell density which were more rapid and extensive than those seen with A-Z-CINN 310 without light or a 10-fold higher concentration of co-administered trastuzumab plus paclitaxel. This suggests that targeted delivery of paclitaxel using A-Z-CINN 310 kills tumor cells by localized release of paclitaxel at the tumor site, which can be accelerated by light treatment. These results indicate that a targeted prodrug therapy containing trastuzumab as the targeting agent and A-Z-CINN-paclitaxel as the prodrug results in a conjugate that is more effective in killing tumor cells than equivalent concentrations of co-administered trastuzumab and paclitaxel. Targeting of a drug can reduce the dose needed for effective therapy and can increase local bioavailability. This makes targeted therapy using an A-Z-CINN prodrug delivery system feasible for treating both primary and metastatic tumors.
Investigations of Factors That Influence the Acrylamide Content of Heated Foodstuffs (2003)

The acrylamide content of heated foodstuffs should be considered to be the net result of complex reactions leading to the formation and elimination/degradation of this compound. The present study, involving primarily homogenized potato heated in an oven, was designed to characterize parameters that influence these reactions, including the heating temperature, duration of heating, pH, and concentrations of various components. Higher temperature (200 degrees C) combined with prolonged heating times produced reduced levels of acrylamide, due to elimination/degradation processes. At certain concentrations the presence of asparagine or monosaccharides (in particular, fructose and also glucose and glyceraldehyde) was found to increase the net content of acrylamide. Addition of other free amino acids or a protein-rich food component strongly reduced the acrylamide content, probably by promoting competing reactions and/or covalently binding acrylamide formed. The dependence on pH of the acrylamide content exhibited a maximum around pH 8; in particular, lower pH was shown to enhance elimination and decelerate formation of acrylamide. In contrast, the effects of additions of antioxidants or peroxides on acrylamide content were small or nonexistent.
Key residues of the receptor binding motif in the spike protein of SARS-CoV-2 that interact with ACE2 and neutralizing antibodies (2020)

Coronavirus disease 2019 (COVID-19), caused by the novel human coronavirus SARS-CoV-2, is currently a major threat to public health worldwide. The viral spike protein binds the host receptor angiotensin-converting enzyme 2 (ACE2) via the receptor-binding domain (RBD), and thus is believed to be a major target to block viral entry. Both SARS-CoV-2 and SARS-CoV share this mechanism. Here we functionally analyzed the key amino acid residues located within receptor binding motif of RBD that may interact with human ACE2 and available neutralizing antibodies. The in vivo experiments showed that immunization with either the SARS-CoV RBD or SARS-CoV-2 RBD was able to induce strong clade-specific neutralizing antibodies in mice; however, the cross-neutralizing activity was much weaker, indicating that there are distinct antigenic features in the RBDs of the two viruses. This finding was confirmed with the available neutralizing monoclonal antibodies against SARS-CoV or SARS-CoV-2. It is worth noting that a newly developed SARS-CoV-2 human antibody, HA001, was able to neutralize SARS-CoV-2, but failed to recognize SARS-CoV. Moreover, the potential epitope residues of HA001 were identified as A475 and F486 in the SARS-CoV-2 RBD, representing new binding sites for neutralizing antibodies. Overall, our study has revealed the presence of different key epitopes between SARS-CoV and SARS-CoV-2, which indicates the necessity to develop new prophylactic vaccine and antibody drugs for specific control of the COVID-19 pandemic although the available agents obtained from the SARS-CoV study are unneglectable.
Modification of plant N-glycans processing: The future of producing therapeutic protein by transgenic plants (2004)

Transgenic plants are regarded as one of the most promising systems for the production of human therapeutic proteins. The number of therapeutic proteins successfully produced in plants is steadily arising. However, the glycoproteins normally produced from plants are not the same as native therapeutic proteins produced from mammals or humans. In addition to in vitro enzymatic modeling glycoproteins, there are two gene manipulation strategies to humanize plant N-glycans connected to the glycoproteins. One is retaining the recombinant glycoproteins in endoplasmic reticulum (ER), the site where few specific modifications of N-glycans occurs. The other is inhibiting the plant endogenous Golgi glycosyltransferase and/or adding new glycosyltransferase from mammalians. In this review, the biosynthesis of N-glycans in plants, the modification of the plant N-glycans processing will be discussed.
MicroRNA gene expression profile of hepatitis C virus–associated hepatocellular carcinoma†‡ (2008)

A subset of microRNAs are aberrantly expressed in primary liver tumors, serving both as putative tumor suppressors and as oncogenic regulators.
Solvent‐Free Synthesis of 6‐Arylbenzimidazo[1,2‐c]quinazolines under Microwave Irradiation. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
PTEN, a unique tumor suppressor gene. (2000)

For many years, it has been thought that the chromosome region 10q22-24 includes one or more genes that appear to play a role in several human malignancies. PTEN is a new tumor suppressor gene encoding a dual-specificity phosphatase that was cloned simultaneously by three groups (Li & Sun 1997, Li et al. 1997, Steck et al. 1997), two of which used a positional cloning approach to identify genes in chromosome 10 (Li et al. 1997, Steck et al. 1997). While several protein kinases have been implicated as oncogenes, and phosphatases have long been known frequently to antagonize their function, there has been no direct demonstration of the role of phosphatases in tumor development (Myers & Tonks 1997). PTEN characterization as a bona fide tumor suppressor gene has confirmed that a deficient phosphatase activity can lead to cancer, as detailed by studies that are described below.
Connective tissue growth factor coordinates chondrogenesis and angiogenesis during skeletal development (2003)

Coordinated production and remodeling of the extracellular matrix is essential during development. It is of particular importance for skeletogenesis, as the ability of cartilage and bone to provide structural support is determined by the composition and organization of the extracellular matrix. Connective tissue growth factor (CTGF, CCN2) is a secreted protein containing several domains that mediate interactions with growth factors, integrins and extracellular matrix components. A role for CTGF in extracellular matrix production is suggested by its ability to mediate collagen deposition during wound healing. CTGF also induces neovascularization in vitro, suggesting a role in angiogenesis in vivo. To test whether CTGF is required for extracellular matrix remodeling and/or angiogenesis during development, we examined the pattern of Ctgf expression and generated Ctgf-deficient mice. Ctgf is expressed in a variety of tissues in midgestation embryos, with highest levels in vascular tissues and maturing chondrocytes. We confirmed that CTGF is a crucial regulator of cartilage extracellular matrix remodeling by generating Ctgf(-/-) mice. Ctgf deficiency leads to skeletal dysmorphisms as a result of impaired chondrocyte proliferation and extracellular matrix composition within the hypertrophic zone. Decreased expression of specific extracellular matrix components and matrix metalloproteinases suggests that matrix remodeling within the hypertrophic zones in Ctgf mutants is defective. The mutant phenotype also revealed a role for Ctgf in growth plate angiogenesis. Hypertrophic zones of Ctgf mutant growth plates are expanded, and endochondral ossification is impaired. These defects are linked to decreased expression of vascular endothelial growth factor (VEGF) in the hypertrophic zones of Ctgf mutants. These results demonstrate that CTGF is important for cell proliferation and matrix remodeling during chondrogenesis, and is a key regulator coupling extracellular matrix remodeling to angiogenesis at the growth plate.