gebhart/patrepeval huggingface dataset:
I.—Some Additions to the Vertebrate Fauna of the Norfolk “Preglacial Forest Bed” with Description of a New Species of Deer (Cervus Rectus) (1889)

Vertebrate remains from the “Forest Bed” continue to be brought to light by the rapid denudation of the East Anglian coast, and I have again to acknowledge my indebtedness to Mr. A. Savin, of Cromer, whose assiduous collecting has preserved so many of these fossils, and made them available for scientific study. One of the specimens which he has now sent me is a species of Cervus , apparently new to science, while the others, although referable to living forms, are now for the first time definitely recorded from the “Forest Bed,” and if my determinations prove to be correct, the following names may be added to the list of Mammalia from this deposit:— Cervus rectus , new species. Bison bonasus , Linn., var. priscus , Bojanus (to replace Bos primigenius ).
Selective inhibition of HIV-1 reverse transcriptase-associated ribonuclease H activity by hydroxylated tropolones (2005)

High-throughput screening of a National Cancer Institute library of pure natural products identified the hydroxylated tropolone derivatives beta-thujaplicinol (2,7-dihydroxy-4-1(methylethyl)-2,4,6-cycloheptatrien-1-one) and manicol (1,2,3,4-tetrahydro-5-7-dihydroxy-9-methyl-2-(1-methylethenyl)-6H-benzocyclohepten-6-one) as potent and selective inhibitors of the ribonuclease H (RNase H) activity of human immunodeficiency virus-type 1 reverse transcriptase (HIV-1 RT). beta-Thujaplicinol inhibited HIV-1 RNase H in vitro with an IC50 of 0.2 microM, while the IC50 for Escherichia coli and human RNases H was 50 microM and 5.7 microM, respectively. In contrast, the related tropolone analog beta-thujaplicin (2-hydroxy-4-(methylethyl)-2,4,6-cycloheptatrien-1-one), which lacks the 7-OH group of the heptatriene ring, was inactive, while manicol, which possesses a 7-OH group, inhibited HIV-1 and E.coli RNases H with IC50 = 1.5 microM and 40 microM, respectively. Such a result highlights the importance of the 2,7-dihydroxy function of these tropolone analogs, possibly through a role in metal chelation at the RNase H active site. Inhibition of HIV-2 RT-associated RNase H indirectly indicates that these compounds do not occupy the nonnucleoside inhibitor-binding pocket in the vicinity of the DNA polymerase domain. Both beta-thujaplicinol and manicol failed to inhibit DNA-dependent DNA polymerase activity of HIV-1 RT at a concentration of 50 microM, suggesting that they are specific for the C-terminal RNase H domain, while surface plasmon resonance studies indicated that the inhibition was not due to intercalation of the analog into the nucleic acid substrate. Finally, we have demonstrated synergy between beta-thujaplicinol and calanolide A, a nonnucleoside inhibitor of HIV-1 RT, raising the possibility that both enzymatic activities of HIV-1 RT can be simultaneously targeted.
Interwoven Metal-Organic Framework on a Periodic Minimal Surface with Extra-Large Pores (2001)

Interpenetration (catenation) has long been considered a major impediment in the achievement of stable and porous crystalline structures. A strategy for the design of highly porous and structurally stable networks makes use of metal-organic building blocks that can be assembled on a triply periodic P-minimal geometric surface to produce structures that are interpenetrating-more accurately considered as interwoven. We used 4,4',4"-benzene-1,3,5-triyl-tribenzoic acid (H(3)BTB), copper(II) nitrate, and N,N'-dimethylformamide (DMF) to prepare Cu(3)(BTB)(2)(H(2)O)(3).(DMF)(9)(H(2)O)(2) (MOF-14), whose structure reveals a pair of interwoven metal-organic frameworks that are mutually reinforced. The structure contains remarkably large pores, 16.4 angstroms in diameter, in which voluminous amounts of gases and organic solvents can be reversibly sorbed.
On the snake in the box problem (1987)

Abstract A snake in a graph is a simple cycle without chords. Denote by s(d) the length of a longest snake in the d-dimensional unit cube. We give a new proof of the theorem of Evdokimov that s(d) > λ2d, where λ is a positive constant.
Ulceration of Pyoderma Gangrenosum Treated with Negative Pressure Wound Therapy (2005)

Pyoderma gangrenosum is a skin disease characterized by wounds with blue-to-purple undermined borders surrounding purulent necrotic bases. This article reports on a patient with a circumferential, full-thickness, and partially necrotic lower-extremity ulceration of unknown etiology. Results of laboratory tests and arterial and venous imaging studies were found to be within normal limits. The diagnosis of pyoderma gangrenosum was made on the basis of the histologic appearance of the wound tissue after biopsy as a diagnosis of exclusion. Negative pressure wound therapy was undertaken, which saved the patient's leg from amputation. Although negative pressure wound therapy has demonstrated efficacy in the treatment of chronic wounds in a variety of circumstances, this is the first documented use of this technique to treat an ulceration secondary to pyoderma gangrenosum.
Incorporation of Porcine Adenovirus 4 Fiber Protein Enhances Infectivity of Adenovirus Vector on Dendritic Cells: Implications for Immune-Mediated Cancer Therapy (2015)

One strategy in cancer immunotherapy is to capitalize on the key immunoregulatory and antigen presenting capabilities of dendritic cells (DCs). This approach is dependent on efficient delivery of tumor specific antigens to DCs, which subsequently induce an anti-tumor T-cell mediated immune response. Human adenovirus serotype 5 (HAdV5) has been used in human studies for gene delivery, but has limited infection in DCs, which lack the proper receptors. Addition of the porcine fiber knob (PK) from porcine adenovirus type 4 to HAdV5 allows the virus to deliver genetic material via binding to glycosylated surface proteins and bypasses the coxsackie-and-adenovirus receptor required by wild-type HAdV5. In this study we explored the potential therapeutic applications of an adenovirus with PK-based tropism against cancers expressing mesothelin. Infectivity and gene transfer assays were used to compare Ad5-PK to wild-type HAdV5. Mouse models were used to demonstrate peptide specificity and T-cell responses. We show that the PK modification highly augmented infection of DCs, including the CD141+ DC subset, a key subset for activation of naïve CD8+ T-cells. We also show that Ad5-PK increases DC infectivity and tumor specific antigen expression. Finally, vaccination of mice with the Ad5-PK vector resulted in enhanced T-cell-mediated interferon gamma (IFN-γ) release in response to both mesothelin peptide and a tumor line expressing mesothelin. Ad5-PK is a promising tool for cancer immunotherapy as it improves infectivity, gene transfer, protein expression, and subsequent T-cell activation in DCs compared to wild-type HAdV5 viruses.
Surface registration for use in interactive, image-guided liver surgery (2000)

This is an initial study considering the use of surface registration for the purpose of physical-to-image registration in the area of liver surgery.
Zn2+-Triggered Amide Tautomerization Produces a Highly Zn2+-Selective, Cell-Permeable, and Ratiometric Fluorescent Sensor (2009)

It is still a significant challenge to develop a Zn(2+)-selective fluorescent sensor with the ability to exclude the interference of some heavy and transition metal (HTM) ions such as Fe(2+), Co(2+), Ni(2+), Cu(2+), Cd(2+), and Hg(2+). Herein, we report a novel amide-containing receptor for Zn(2+), combined with a naphthalimide fluorophore, termed ZTRS. The fluorescence, absorption detection, NMR, and IR studies indicated that ZTRS bound Zn(2+) in an imidic acid tautomeric form of the amide/di-2-picolylamine receptor in aqueous solution, while most other HTM ions were bound to the sensor in an amide tautomeric form. Due to this differential binding mode, ZTRS showed excellent selectivity for Zn(2+) over most competitive HTM ions with an enhanced fluorescence (22-fold) as well as a red-shift in emission from 483 to 514 nm. Interestingly, the ZTRS/Cd(2+) complex showed an enhanced (21-fold) blue-shift in emission from 483 to 446 nm. Therefore, ZTRS discriminated in vitro and in vivo Zn(2+) and Cd(2+) with green and blue fluorescence, respectively. Due to the stronger affinity, Zn(2+) could be ratiometrically detected in vitro and in vivo with a large emission wavelength shift from 446 to 514 nm via a Cd(2+) displacement approach. ZTRS was also successfully used to image intracellular Zn(2+) ions in the presence of iron ions. Finally, we applied ZTRS to detect zinc ions during the development of living zebrafish embryos.
Volumetric transformation of brain anatomy (1997)

This paper presents diffeomorphic transformations of three-dimensional (3-D) anatomical image data of the macaque occipital lobe and whole brain cryosection imagery and of deep brain structures in human brains as imaged via magnetic resonance imagery. These transformations are generated in a hierarchical manner, accommodating both global and local anatomical detail. The initial low-dimensional registration is accomplished by constraining the transformation to be in a low-dimensional basis. The basis is defined by the Green's function of the elasticity operator placed at predefined locations in the anatomy and the eigenfunctions of the elasticity operator. The high-dimensional large deformations are vector fields generated via the mismatch between the template and target-image volumes constrained to be the solution of a Navier-Stokes fluid model. As part of this procedure, the Jacobian of the transformation is tracked, insuring the generation of diffeomorphisms. It is shown that transformations constrained by quadratic regularization methods such as the Laplacian, biharmonic, and linear elasticity models, do not ensure that the transformation maintains topology and, therefore, must only be used for coarse global registration.
Molecular characterization of a maize B chromosome centric sequence. (1993)

Supernumerary chromosomes are widespread in the plant kingdom but little is known of their molecular nature or mechanism of origin. We report here the initial cloning of sequences from the maize B chromosome. Our analysis suggests that many sequences are highly repetitive and shared with the normal A chromosomes. However, all clones selected for B-specificity contain at least one copy of a particular repeat. Cytological mapping using B chromosome derivatives and in situ hybridization show that the B specific repeats are derived from the centric region of the chromosome. Sequence analysis of this repeat shows homology to motifs mapped to various plant and animal centromeres and to the maize neocentromere. A precise localization of these sequences among breakpoints within the B centromere and an homology to a facultative centromere, suggest a role for this sequence in centromere function.
Bacteriophage treatment of suppurative skin infections. (1987)

The study material comprised 31 patients with chronic suppurative infections of the skin caused by Pseudomonas, Staphylococcus, Klebsiella, Proteus and Escherichia. Within 2-16 weeks of the treatment, an improvement of the general state was observed as well as suppression of the local inflammation, purification of a wound from the suppurative and necrotic content, faster healing of the ulcers and fully negative results of the bacteriologic tests. In 16 cases, an outstanding therapeutic effect was obtained, in 7 cases marked improvement was reported and in 2 a transitory improvement was reported. In 7 patients the treatment was abandoned due to the lack of improvement (1 case) or development of side effects (6 cases). The results obtained provide evidence for the high effectiveness of phage therapy in the treatment of suppurative skin infections.
Mismatch-containing oligonucleotide duplexes bound by theE.coli mutS-encoded protein (1988)

The binding of the mutS gene product, a protein involved in at least two E. coli mismatch correction pathways, to a series of synthetic DNA duplexes containing mismatches or mismatch analogues of the purine/pyrimidine type was studied in order to establish whether a correlation exists between the recognition of these mispairs and the efficiency of their correction in vivo. Experiments using nitrocellulose filter binding or band-shift assays revealed that duplexes containing a G/T mismatch or its analogues I/T and DI/T were bound by the protein with affinities correlating to the efficiency of their repair in vivo. In contrast, the A/C mismatch, contained within the same sequence, was bound only poorly, despite being efficiently corrected in vivo. The analogues of the A/C mispair, uncorrected in vivo, were not detectably bound under the conditions of these assays.
Mitochondrial coenzyme Q content and aging (1999)

The main objective of this study was to determine the nature of the relationship between aging and mitochondrial coenzyme Q (CoQ) content. Mitochondria in the heart, skeletal muscle, kidney and brain of the mouse varied in both the amount of total CoQ (CoQ9 + CoQ10) content as well as in the ratio of the CoQ9 to CoQ10. CoQ content declined with age only in the skeletal muscle. Caloric restriction (CR) resulted in an increase in the amount of CoQ9 in skeletal muscle mitochondria. This effect was partially reversible upon termination of the caloric restriction regimen. Results suggest that a decrease in mitochondrial CoQ content is an integral aspect of aging in skeletal muscle.
Compositional bias and mimicry toward the nonself proteome in immunodominant T cell epitopes of self and nonself antigens (2000)

We investigated whether and how molecular mimicry affects the shaping of the helper T cell repertoire. We implemented an algorithm that measures the probability of mimicry between epitopes of known immunogenicity and self or nonself proteomes. This algorithm yields 'similarity profiles', which represent the probability of matching between all contiguous overlapping peptides of the antigen under examination and those in the proteome(s) considered. Similarity profiles between helper T cell epitopes (of self or microbial antigens and allergens) and human or microbial SWISSPROT collections were produced. For each antigen, both collections yielded largely overlapping profiles, demonstrating that self-nonself discrimination does not rely on qualitative features that distinguish human from microbial peptides. However, epitopes whose probability of mimicry with self or nonself prevails are, respectively, tolerated or immunodominant and coexist within the same (auto-)antigen regardless of its self/nonself nature. Epitopes (on self and nonself antigens) can cross-stimulate T cells at increasing potency as their similarity with nonself augments. Mimicry, rather than complicating self-nonself discrimination, assists in the shaping of the immune repertoire and helps define the defensive or autoreactive potential of a T cell. Being a predictor of epitope immunogenicity, it bears relevance to vaccine design.
PKCδ Alternatively Spliced Isoforms Modulate Cellular Apoptosis in Retinoic Acid-Induced Differentiation of Human NT2 Cells and Mouse Embryonic Stem Cells (2006)

NT2 cells are a human teratocarcinoma cell line that, upon treatment with retinoic acid (RA), begin differentiating into a neuronal phenotype. The transformation of undifferentiated NT2 cells into hNT neurons presents an opportunity to investigate the mechanisms involved in neurogenesis because a key component is cell apoptosis, which is essential for building neural networks. Protein kinase Cdelta (PKCdelta) plays an important role as a mediator of cellular apoptosis in response to various stimuli. PKCdelta (deltaI) is proteolytically cleaved at its hinge region (V3) by caspase 3 and the catalytic fragment is sufficient to induce apoptosis in various cell types. Mouse PKCdeltaII is rendered caspase resistant due to an insertion of 78 bp within the caspase recognition site in its V3 domain. No functional role has been attributed to these alternatively spliced variants of PKCdelta. We sought to find a correlation between the onset of apoptosis, neurogenesis, and the expression of PKCdelta isoforms. Our results indicate that RA regulates the expression of PKCdelta alternative splicing variants in NT2 cells. Further, overexpression of PKCdeltaI promotes apoptosis while PKCdeltaII overexpression shields the cells from apoptosis. This is the first report to attribute physiological function to PKCdeltaI and -deltaII isoforms. Next we demonstrated that mouse embryonic stem cells differentiate in vitro into dopaminergic neurons upon stimulation with RA and ciliary neurotrophic factor. These cells showed a simultaneous increase in tyrosine hydroxylase and PKCdeltaII expression. We suggest that the molecular mechanisms regulating differentiation and apoptosis could be understood by alternative expression of PKCdelta isoforms.
Opportunities for microfluidic technologies in synthetic biology (2009)

We introduce microfluidics technologies as a key foundational technology for synthetic biology experimentation. Recent advances in the field of microfluidics are reviewed and the potential of such a technological platform to support the rapid development of synthetic biology solutions is discussed.
Correction: Genetic Variation in Interleukin 28B and Response to Antiviral Therapy in Patients with Dual Chronic Infection with Hepatitis B and C Viruses (2013)

Concurrent infection with hepatitis C virus (HCV) and hepatitis B virus (HBV) was not uncommon in China. To date, information on predictors of response to treatment of dually-infected HCV/HBV is limited. The aim of this study was to evaluated whether determination of the interleukin 28B (IL-28B) polymorphism statuses sufficient to predict treatment response of interferon (IFN)-based therapy in patients chronically infected with both hepatitis B and C viruses. We investigated the role of IL28B variations (rs8099917 and rs12979860) in response to IFN-based treatment and evaluated its association with the risk of the null virological response (NVR) in HCV /HBV dually-infected patients. We found that the overall distributions of the genotypes among the sustained virological response (SVR), NVR groups were significantly different (P<0.001): patients with the rs8099917 TG genotype had an increased risk of NVR (odds ratio [OR] =2.37 95% confidence interval [CI] =1.16-4.83, P =0.017), and those with the GG genotype had a further increased risk of NVR (OR=4.23, 95% CI =1.17-15.3, P=0.027). The rs12979860 allele was also highly associated with treatment failure (CT/TT vs. CC; OR =2.04, 95%CI =1.05-3.97, P =0.037). Moreover, we found that IL28B rs8099917 G variants (TG+GG) interact with HCV genotype 1(G1) to result in higher risk of NVR (P=0.009), and that they are also associated with HBV DNA reactivation (TG+GG vs. TT, P=0.005). Furthermore, multivariate regression analysis show that the rs8099917 G allele was the most important factor significantly associated with a NVR in HCV G1 patients. This study suggest that IL28B genotyping may be a valid pretreatment predictor of which patients are likely to respond to treatment in this group of difficult-to-treat HCV/HBV dually-infected patients.
TGF-β1expression and angiogenesis in colorectal cancer tissue (2002)

TGF beta(1) might be associated with tumor progression by modulating the angiogenesis in colorectal cancer and TGF beta(1) may be used as a possible biomarker.
Chronic obstructive pulmonary disease: treatment (Part Two) (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
THE EFFECT OF CELLS TRANSFERRED INTO THE MOUSE BLASTOCYST ON SUBSEQUENT DEVELOPMENT (1974)

Bone marrow cells from CBA T6T6 mice and testicular teratocarcinoma cells from 129 SvSl mice were transferred into blastocysts from random-bred Swiss albino mice. The blastocysts were allowed to develop in foster mothers and the adults resulting from these blastocysts were studied for evidence of an effect of the transferred cells. A total of 137 adults resulted from the experiments, and one of the mice that had received teratocarcinoma cells in the blastocyst stage showed several thin stripes of agouti hair. All the adult animals received grafts of skin from animals identical to those supplying the cells. In all cases the animals that resulted from blastocysts into which cells had been transferred maintained skin grafts for a significantly longer period than controls. In a number of cases the graft developed agouti hair and in two cases the graft was maintained for approximately 2 mo. These experiments indicate that the transferred cells were able to establish small colonies in the embryos and that some of these cells persisted into the adult.
Compression of acoustic features for speech recognition in network environments (2002)

In this paper, we describe a new compression algorithm for encoding acoustic features used in typical speech recognition systems. The proposed algorithm uses a combination of simple techniques, such as linear prediction and multi-stage vector quantization, and the current version of the algorithm encodes the acoustic features at a fixed rate of 4.0 kbit/s. The compression algorithm can be used very effectively for speech recognition in network environments, such as those employing a client-server model, or to reduce storage in general speech recognition applications. The algorithm has also been tuned for practical implementations, so that the computational complexity and memory requirements are modest. We have successfully tested the compression algorithm against many test sets from several different languages, and the algorithm performed very well, with no significant change in the recognition accuracy due to compression.
Building efficient and effective metasearch engines (2002)

Frequently a user's information needs are stored in the databases of multiple search engines. It is inconvenient and inefficient for an ordinary user to invoke multiple search engines and identify useful documents from the returned results. To support unified access to multiple search engines, a metasearch engine can be constructed. When a metasearch engine receives a query from a user, it invokes the underlying search engines to retrieve useful information for the user. Metasearch engines have other benefits as a search tool such as increasing the search coverage of the Web and improving the scalability of the search. In this article, we survey techniques that have been proposed to tackle several underlying challenges for building a good metasearch engine. Among the main challenges, the database selection problem is to identify search engines that are likely to return useful documents to a given query. The document selection problem is to determine what documents to retrieve from each identified search engine. The result merging problem is to combine the documents returned from multiple search engines. We will also point out some problems that need to be further researched.
Comparing image-based localization methods (2003)

This paper compares alternative approaches to pose estimation using visual cues from the environment. We examine approaches that derive pose estimates from global image properties, such as principal components analysis (PCA) versus from local image properties, commonly referred to as landmarks. We also consider the failure-modes of the different methods. Our work is validated with experimental results. 1