gebhart/patrepeval huggingface dataset:
Growth and Early Postimplantation Defects in Mice Deficient for the Bromodomain-Containing Protein Brd4 (2002)

In a gene trap screen we recovered a mouse mutant line in which an insertion generated a null allele of the Brd4 gene. Brd4 belongs to the Fsh/Brd family, a group of structurally related proteins characterized by the association of two bromodomains and one extraterminal domain. Members of this family include Brd2/Ring3/Fsrg1 in mammals, fs(1)h in Drosophila, and Bdf1 in Saccharomyces cerevisiae. Brd4 heterozygotes display pre- and postnatal growth defects associated with a reduced proliferation rate. These mice also exhibit a variety of anatomical abnormalities: head malformations, absence of subcutaneous fat, cataracts, and abnormal liver cells. In primary cell cultures, heterozygous cells also display reduced proliferation rates and moderate sensitivity to methyl methanesulfonate. Embryos nullizygous for Brd4 die shortly after implantation and are compromised in their ability to maintain an inner cell mass in vitro, suggesting a role in fundamental cellular processes. Finally, sequence comparisons suggest that Brd4 is likely to correspond to the Brd-like element of the mediator of transcriptional regulation isolated by Y. W. Jiang, P. Veschambre, H. Erdjument-Bromage, P. Tempst, J. W. Conaway, R. C. Conaway, and R. D. Kornberg (Proc. Natl. Acad. Sci. USA 95:8538-8543, 1998) and the Brd4 mutant phenotype is discussed in light of this result. Together, our results provide the first genetic evidence for an in vivo role in mammals for a member of the Fsh/Brd family.
Fast and efficient algorithms for text and video compression (1997)

One limitation of reduced-intensity preparative regimens is potential for graft failure. We have developed a regimen that targets CD4(+) lymphodepletion to ensure early and durable engraftment. The primary endpoint was achievement of ≥50% CD3(+) donor chimerism by day +28. Forty-two patients (median age, 53 years; range, 29 to 73 years) received pentostatin 4 mg/m(2) i.v. on days -28, -21, and -14 when the CD4(+) cell count was >100 cells/μL and on days -4 and -3 regardless of CD4(+) level. Rituximab 375 mg/m(2) was administered to patients with CD20(+) malignancies on days -21, -14, -7, +1, and +8. Busulfan 200 mg/m(2) i.v. was administered on days -4 and -2 at a dose to target a cumulative AUC dose of 16,000 (±10%) μmol·min/L. Graft-versus-host disease (GVHD) prophylaxis consisted of tacrolimus plus methotrexate in 86% of patients. Donors were matched-related (47%), matched unrelated (43%), or mismatched unrelated (10%). Chronic lymphocytic leukemia (45%) and follicular non-Hodgkin lymphoma (14%) were the most common diagnoses. Disease status at initiation of the preparative regimen was complete remission in 22%, partial response in 55%, and stable/progression in 24%. The median percent CD4(+) cell count decrease from baseline (day -28) was 52% to day -21, 66% to day -14, 62% to day -7, and 91% to day 0. At day +28, all 42 patients (100%) had ≥50% CD3(+) donor chimerism. No patient experienced graft failure. Overall response rate was 82% (complete remisson, 67%). The day +100 cumulative incidence of grade II-IV acute GVHD was 59% (grade III-IV acute GVHD, 19%), and the 2 year cumulative incidence of chronic GVHD was 69% (moderate/severe, 58%). Nonrelapse mortality was 2% at day +100 and 17% at 2 years. Two-year PFS was 55%, and OS was 68%. This regimen ensures durable engraftment, is effective against persistent disease, and results in relatively low mortality from causes other than relapse.
The influence of induced micromovement upon the healing of experimental tibial fractures (1985)

Although it has been well established that fracture healing is influenced by the mechanical environment, the optimal parameters have not yet been established. In two groups of sheep an experimental tibial diaphysial fracture was created, and stabilised using external skeletal fixation. In one group rigid fixation was maintained throughout fracture healing; in the other group controlled axial micromovement, with a loading regime known to be osteogenic in intact bones, was applied for a short period daily. A significant improvement in healing was associated with the application of controlled micromovement. Data from these experiments provide the basis for improving the conditions for fracture healing and may assist in the prevention of delayed union.
Do thumbnail previews help users make better relevance decisions about web search results? (2002)

We describe an empirical evaluation of the utility of thumbnail previews in web search results. Results pages were constructed to show text-only summaries, thumbnail previews only, or the combination of text summaries and thumbnail previews. We found that in the combination case, users were able to make more accurate decisions about the potential relevance of results than in either of the other versions, with hardly any increase in speed of processing the page as a whole.
Endocytic Recycling is Required for the Presentation of an Exogenous Peptide via MHC Class II Molecules (2000)

Exogenous antigenic peptides captured and presented in the context of major histocompatibility (MHC) class II molecules on APC, have been employed as potent vaccine reagents capable of activating cellular immune responses. Binding and presentation of select peptide via surface class II molecules has been reported. Here, a role for endocytosis and early endosomes in the presentation of exogenous peptides via MHC class II molecules is described. T cell recognition of a 14 amino acid human serum albumin-derived peptide in the context of HLA-DR4 was observed only with metabolically active APC. The delayed kinetics and temperature dependence of functional peptide presentation via APC, were consistent with a requirement for peptide internalization to early endosomal compartments prior to T cell recognition. Ablating endocytosis by exposing cells to inhibitors of ATP production completely blocked the display of functional peptide:class II complexes on the surface of the APC. Presentation of the peptide was also found to be sensitive to primaquine, a drug that perturbs the recycling of transport vesicles containing endocytic receptors and mature class II complexes. Functional presentation of the endocytosed peptide was dependent upon these mature class II complexes, as inhibitor studies ruled out a requirement for newly synthesized class II molecules. N-terminal processing of the endocytosed peptide was observed upon trafficking through endosomal compartments and linked to the formation of functional peptide:class II complexes. These findings establish a novel mechanism for regulating class II-restricted peptide presentation via the endocytic pathway.
Xylanases: from Biology to BioTechnology (1996)

Xylan is the main carbohydrate found in the hemicellulosic fraction of plant tissues and accounts for one third of all renewable organic carbon available on earth. Xylanase, the major component of an enzymatic consortium, acts in nature by depolymerizing xylan molecules into monomeric pentosan units that are used by bacterial and fungal populations as a primary carbon source. Xylanase producers have been isolated from all ecological niches where plant material is deposited, and microorganisms often contain multiple loci encoding overlapping xylanolytic functions. The numerical excess of genes and the extensive sharing of structural features within beta-glycanase families suggests that extensive gene duplication and conversion events have occurred during xylanase evolution. Hydrolysis of beta-glycosidic linkages is sponsored by a general acid catalytic reaction common to all glycanases, whereas substrate recognition is specified by subsites that interact with adjacent glycosyl units. Under natural conditions xylanases are inducible by the products of their own action and subject to carbon catabolite repression. Bleaching paper pulps with xylanases is the first successful commercial application for these enzymes. The recovery of cellulosic textile fibers is the next logical application and bioconversion of biomass into fuels and chemicals, remains the ultimate target. Recent developments have shown that metabolic pathways can be transferred from one organism to another and proteins can be modified to gain conformational stability, suggesting that naturally occurring systems can be custom engineered to the situation in the fermentation tank. Thus, biotechnologies developed to transform biomass into marketable products that gradually substitute materials derived from non-renewable resources are becoming commercially worthwhile.
Suppression of retinal neovascularization in vivo by inhibition of vascular endothelial growth factor (VEGF) using soluble VEGF-receptor chimeric proteins. (1995)

The majority of severe visual loss in the United States results from complications associated with retinal neovascularization in patients with ischemic ocular diseases such as diabetic retinopathy, retinal vein occlusion, and retinopathy of prematurity. Intraocular expression of the angiogenic protein vascular endothelial growth factor (VEGF) is closely correlated with neovascularization in these human disorders and with ischemia-induced retinal neovascularization in mice. In this study, we evaluated whether in vivo inhibition of VEGF action could suppress retinal neovascularization in a murine model of ischemic retinopathy. VEGF-neutralizing chimeric proteins were constructed by joining the extracellular domain of either human (Flt) or mouse (Flk) high-affinity VEGF receptors with IgG. Control chimeric proteins that did not bind VEGF were also used. VEGF-receptor chimeric proteins eliminated in vitro retinal endothelial cell growth stimulation by either VEGF (P < 0.006) or hypoxic conditioned medium (P < 0.005) without affecting growth under nonstimulated conditions. Control proteins had no effect. To assess in vivo response, animals with bilateral retinal ischemia received intravitreal injections of VEGF antagonist in one eye and control protein in the contralateral eye. Retinal neovascularization was quantitated histologically by a masked protocol. Retinal neovascularization in the eye injected with human Flt or murine Flk chimeric protein was reduced in 100% (25/25; P < 0.0001) and 95% (21/22; P < 0.0001) 0.0001) of animals, respectively, compared to the control treated eye. This response was evident after only a single intravitreal injection and was dose dependent with suppression of neovascularization noted after total delivery of 200 ng of protein (P < 0.002). Reduction of histologically evident neovascular nuclei per 6-microns section averaged 47% +/- 4% (P < 0.001) and 37% +/- 2% (P < 0.001) for Flt and Flk chimeric proteins with maximal inhibitory effects of 77% and 66%, respectively. No retinal toxicity was observed by light microscopy. These data demonstrate VEGF's causal role in retinal angiogenesis and prove the potential of VEGF inhibition as a specific therapy for ischemic retinal disease.
Control of hair growth and follicle size by VEGF-mediated angiogenesis (2001)

The murine hair follicle undergoes pronounced cyclic expansion and regression, leading to rapidly changing demands for its vascular support. Our study aimed to quantify the cyclic changes of perifollicular vascularization and to characterize the biological role of VEGF for hair growth, angiogenesis, and follicle cycling. We found a significant increase in perifollicular vascularization during the growth phase (anagen) of the hair cycle, followed by regression of angiogenic blood vessels during the involution (catagen) and the resting (telogen) phase. Perifollicular angiogenesis was temporally and spatially correlated with upregulation of VEGF mRNA expression by follicular keratinocytes of the outer root sheath, but not by dermal papilla cells. Transgenic overexpression of VEGF in outer root sheath keratinocytes of hair follicles strongly induced perifollicular vascularization, resulting in accelerated hair regrowth after depilation and in increased size of hair follicles and hair shafts. Conversely, systemic treatment with a neutralizing anti-VEGF antibody led to hair growth retardation and reduced hair follicle size. No effects of VEGF treatment or VEGF blockade were observed in mouse vibrissa organ cultures, which lack a functional vascular system. These results identify VEGF as a major mediator of hair follicle growth and cycling and provide the first direct evidence that improved follicle vascularization promotes hair growth and increases hair follicle and hair size.
Homology of the 70-kilodalton antigens from Mycobacterium leprae and Mycobacterium bovis with the Mycobacterium tuberculosis 71-kilodalton antigen and with the conserved heat shock protein 70 of eucaryotes (1989)

Two lambda gt11 recombinant clones, JKL2 and JKL15, each containing an insert coding for part of the highly immunogenic 70-kilodalton (kDa) protein antigen, were isolated from a Mycobacterium leprae genomic library by immunoscreening with the monoclonal antibody L7. Clone JKL2 contained the largest insert, 2.3 kilobase pairs. Nonoverlapping fragments of this insert were used as probes and showed strong hybridization to a number of Mycobacterium tuberculosis-lambda gt11 recombinants producing proteins recognized by an anti-M. tuberculosis 71-kDa monoclonal antibody, IT11. One clone from a recombinant Mycobacterium bovis library was also characterized by using L7, and the insert from this clone, B5bt, hybridized strongly to the M. leprae probes as well. The nucleotide sequence of the 1,037-base-pair coding region of the JKL2 M. leprae clone which encodes the carboxy-terminal half of the 70-kDa protein had extensive homology with genes from a number of species. In all cases, these genes, including the recently described Ag63 and Ag361 of Plasmodium falciparum, were found to be members of the heat shock protein 70 (hsp 70) family of genes. At the amino acid level, homology was maximal between amino acids 83 through 107 and 159 through 184, which showed extreme conservation (92 and 85% identity) with Escherichia coli DnaK amino acids 386 through 409 and 460 through 485, respectively, and was 51% homologous over the entire coding region (amino acids 1 through 344 of JKL2). In contrast, amino acids 129 through 158 had maximal homology with the phylogenetically more distant Xenopus laevis hsp70. Homology declined substantially in the carboxy-terminal 34 amino acids. The predicted ATP-binding functional activity of the 70-kDa antigen from M. bovis was confirmed with affinity purification of the antigen by binding to ATP-agarose and elution with ATP. In view of the conservation of sequences between these mycobacterial antigens and mammalian endogenous cellular enzymes, further evaluation of these molecules in vivo may aid in understanding tolerance to self-antigens as well as provide potentially useful immunodiagnostic reagents.
Fractionation of antibodies to L-cell colony-stimulating factor by affinity chromatography (1979)

Purified L-cell colony-stimulating factor (CSF) was coupled to cyanogen- bromide-activated Sepharose and used to selectively fractionate antibodies to this factor. With the use of a simplified two-step washing and elution technique, there was 50%--70% binding of the anti- CSF, with recovery of 60%--100% of the bound material. Both the native antiserum and purified anti-CSF fractions were inhibitory to murine granulocyte-macrophage colony formation. The purified antibodies contained only IgG and were reduced in protein concentration to 0.1% of the serum IgG values. These fractions should prove useful tools for the study of granulocyte and macrophage differentiation.
Synthesis of a radiotracer for studying nicotinic acetylcholine receptors: (+/−)-exo-2-(2-[18F]fluoro-5-pyridyl)-7-azabicyclo[2.2.1]heptane (1996)

The radiochemical synthesis of (+/−)-exo-2-(2-[18F]fluoro-5-pyridyl)-7-azabicyclo[2.2.1]heptane ([18F](UNDERLINE)1(/UNDERLINE)) was accomplished by Kryptofix® 222 assisted nucleophilic no-carrier-added [18F]fluorination of (+/−)-exo-2-(2-bromo-5-pyridyl)-7-azabicyclo[2.2.1] heptane ((UNDERLINE)3a(/UNDERLINE)). The average radiochemical yield of the final product was 10% and the average specific activity was greater than >2000 mCi/μmol, calculated at end-of-synthesis. The stable fluorine ligand ([19F](UNDERLINE)1(/UNDERLINE)) was prepared by Kryptofix® 222 assisted nucleophilic fluorination of (+/−)-exo-2-(2-bromo-5-pyridyl) - 7 -methoxycarbonyl - 7 - azabicyclo[2.2.1]heptane ((UNDERLINE)3b(/UNDERLINE)) followed by acid deprotection.
Mesenchymal Stem Cell Transition to Tumor-Associated Fibroblasts Contributes to Fibrovascular Network Expansion and Tumor Progression (2009)

Our results suggest the dependence of in vitro Skov-3 tumor cell proliferation is due to the presence of tumor-stimulated MSC secreted IL6. The subsequent TAF phenotype arises from the MSC which ultimately promotes tumor growth through the contribution of microvascularization, stromal networks, and the production of tumor-stimulating paracrine factors.
Broadband Wireless Access (2002)

From the Publisher:
This book discusses the design, performance and implementation of access protocols with emphasis on how such protocols can efficiently support disparate classes of multimedia traffic. These protocols are deployed or experimented in various broadband wireless environments such as wireless ATM, satellite networks, mobile cellular and personal communication systems, wireless local loops, wireless local area networks, and others. Besides a comprehensive introduction and survey to the evolution of access protocols, some of the hottest topics of current interest are covered. These include: 

Connection control and QoS provisioning. Traffic load balancing techniques. Developments in advanced CDMA/TDMA/OFDM systems. International standardization efforts (e.g., 3G, IMT 2000). Emerging broadband wireless access (e.g., wireless ATM, satellite ATM, high-speed wireless LANs). The complete design, performance analysis, simulation and protocol verification of a generalized broadband multiple access protocol. 


While engineering aspects are discussed, the emphasis is on the physical understanding of access protocols, from basic proposals to the latest innovations. Mathematical treatment is kept to a minimum, and most of the fundamental concepts are explained based on intuition and insights, supplemented by numerous illustrative figures. In addition, these concepts are expressed succinctly and concisely. Wherever possible, important references that make major contributions to the field are included for interested readers to investigate further. Latest updates and useful Web resources are posted at the book's Web site.
Identification and characterization of a new beta-glucoside utilization system in Bacillus subtilis (1997)

A new catabolic system in Bacillus subtilis involved in utilization of beta-glucosidic compounds has been investigated. It consists of five genes encoding phosphotransferase system (PTS) enzyme II (licB and licC) and enzyme IIA (licA), a presumed 6-phospho-beta-glucosidase (licH), as well as a putative regulator protein (licR). The genes map around 334 degrees of the B. subtilis chromosome, and their products are involved in the uptake and utilization of lichenan degradation products. These five genes are organized in two transcriptional units. A weak promoter precedes gene licR, and transcription is obviously terminated at a secondary structure immediately downstream of the reading frame, as shown by Northern RNA blot analysis. Genes licB, licC, licA, and licH constitute an operon. Initiation of transcription at the promoter in front of this operon presumably requires activation by the gene product of licR. The LicR protein shows an unusual domain structure, i.e., similarities to (i) the conserved transcriptional antiterminator BgIG family signature and (ii) PTS enzyme II. Using RNA techniques and transcriptional lacZ fusions, we have shown that the expression of the licBCAH operon is inducible by products of lichenan hydrolysis, lichenan and cellobiose. The presence of excess glucose prevents the induction of this operon, indicating the control by carbon catabolite repression. Moreover, the expression of the operon requires the general PTS components and seems to be negatively controlled by the specific lic PTS enzymes.
Charge Detection Mass Spectrometry for Single Ions with an Uncertainty in the Charge Measurement of 0.65 e (2015)

Charge detection mass spectrometry (CDMS) provides a direct measure of the mass of individual ions through nondestructive, simultaneous measurements of the mass to charge ratio and the charge. To improve the accuracy of the charge measurement, ions are trapped and recirculated through the charge detector. By substantially extending the trapping time, the uncertainty in the charge determination has been reduced by a factor of two, from 1.3 elementary charges (e) to 0.65 e. The limit of detection (the smallest charge that can be reliably measured) has been reduced by about the same proportion, from 13 to 7 e. The more precise charge measurements enable a substantial improvement in the mass resolution, which is critical for applications of CDMS to mixtures of high mass ions.
Novel Benzoxazole 2,4-Thiazolidinediones as Potent Hypoglycemic Agents. Synthesis and Structure-Activity Relationships. (1997)

A new series of benzoxazole 2,4-thiazolidinediones was synthesized and evaluated for hypoglycemic activity in genetically obese and diabetic yellow KK mice. 2-Arylmethyl- and 2-(heteroarylmethyl)benzoxazole derivatives showed far more potent activity than known 2,4-thiazolidinedione derivatives such as ciglitazone, troglitazone and pioglitazone. A facile synthesis of benzoxazole 2,4-thiazolidinediones was also established using aminophenol 2,4-thiazolidinedione (11) as a key intermediate. Details of synthesis and structure-activity relationships for this series are described.
Camera calibration method under poor lighting condition in factories (2008)

This paper proposes a method to perform accurate camera calibration under poor lighting condition of factories or industrial fields. Preprocessing of camera calibration required for measuring object dimensions has to be able to extract calibration points from patterns of the calibration scale, for example, the calibration from plane pattern scale needs at least seven points of the known dimension marked on the scale. However, industrial fields hardly provide proper lighting condition for camera calibration of the measurement system. The data points for calibration are automatically selected from a probabilistic assumption for size variation of the calibration point when the threshold level changes for image binarization. The system requires user to provide at least four points that are incomplete, these points are used to predict position of exact calibration points and extract accurate calibration parameters in an iterative procedure using nonlinear optimization of the parameters. From real images, we prove the method can be applied to camera calibration of poor quality images obtained under lens distortion and bad illumination.