gebhart/patrepeval huggingface dataset:
Friendship and mobility (2011)

Even though human movement and mobility patterns have a high degree of freedom and variation, they also exhibit structural patterns due to geographic and social constraints. Using cell phone location data, as well as data from two online location-based social networks, we aim to understand what basic laws govern human motion and dynamics. We find that humans experience a combination of periodic movement that is geographically limited and seemingly random jumps correlated with their social networks. Short-ranged travel is periodic both spatially and temporally and not effected by the social network structure, while long-distance travel is more influenced by social network ties. We show that social relationships can explain about 10% to 30% of all human movement, while periodic behavior explains 50% to 70%. Based on our findings, we develop a model of human mobility that combines periodic short range movements with travel due to the social network structure. We show that our model reliably predicts the locations and dynamics of future human movement and gives an order of magnitude better performance than present models of human mobility.
Novel microRNA-based assay demonstrates 92% agreement with diagnosis based on clinicopathologic and management data in a cohort of patients with carcinoma of unknown primary (2013)

This novel microRNA-based assay shows high accuracy in identifying the final clinical diagnosis in a real life CUP patient cohort and could be a useful tool to facilitate administration of optimal therapy.
Crystal Structure of the Human Estrogen Sulfotransferase-PAPS Complex (2002)

Estrogen sulfotransferase (EST) transfers the sulfate group from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to estrogenic steroids. Here we report the crystal structure of human EST (hEST) in the context of the V269E mutant-PAPS complex, which is the first structure containing the active sulfate donor for any sulfotransferase. Superimposing this structure with the crystal structure of hEST in complex with the donor product 3'-phosphoadenosine 5'-phosphate (PAP) and the acceptor substrate 17beta-estradiol, the ternary structure with the PAPS and estradiol molecule, is modeled. These structures have now provided a more complete view of the S(N)2-like in-line displacement reaction catalyzed by sulfotransferases. In the PAPS-bound structure, the side chain nitrogen of the catalytic Lys(47) interacts with the side chain hydroxyl of Ser(137) and not with the bridging oxygen between the 5'-phosphate and sulfate groups of the PAPS molecule as is seen in the PAP-bound structures. This conformational change of the side chain nitrogen indicates that the interaction of Lys(47) with Ser(137) may regulate PAPS hydrolysis in the absences of an acceptor substrate. Supporting the structural data, the mutations of Ser(137) to cysteine and alanine decrease gradually k(cat) for PAPS hydrolysis and transfer activity. Thus, Ser(137) appears to play an important role in regulating the side chain interaction of Lys(47) with the bridging oxygen between the 5'-phosphate and the sulfate of PAPS.
Spectroscopic Gradients in Elliptical Galaxies (1995)

Preliminary results based on a large compilation of line-strength profiles are presented and discussed. Elliptical galaxies (Es) with strong central Mg_2 show steeper line-strength gradients. These galaxies are more massive and have higher velocity dispersions, note nevertheless, that the Mg_2 gradient correlates better with central Mg_2 than with any other global or structural parameter. This correlation, and the fact that Mg_2 measures Z/Z_\\odot together with the [Mg/Fe] abundances among Es, are of extreme importance for the use of the central Mg_2-\\sigma relation as a reflection of a mass-metallicity relation. Spectroscopic gradients arise mainly from a radial decrease in mean stellar metallicity. However, the Mg_2 and &lt;{\\rm Fe}&gt; gradients do not correlate within measuring errors, indicating that something else, besides metallicity, is also varying within a galaxy. H\\beta gradients indicate that the centers of Es tend to look spectroscopically ``younger'' than their stellar populations further out.
Shale Barrier Effects on the SAGD Performance (2009)

The SAGD process has already been implemented for commercial production in Alberta Oil Sands areas in Western Canada since early 2000. SAGD performance is very sensitive to reservoir heterogeneities such as shale barriers, bottom and/or top water zones, and a gas cap. In the SAGD process, low permeability zones such as shale layers may act as a flow barrier depending on their size, vertical and horizontal locations, and continuity throughout the reservoir thus making it very important to understand and characterize the effect of shale layers. In this study, the impact of various sizes and locations of shale barriers have been investigated through two-dimensional hypothetical simulation models. The various simulation models have been designed to investigate the shale size and vertical location in both BIP (shale between the injector and producer) and AP (shale above the producer) cases. Two different types of models were designed to look at the effect of flow path existence between the injector and producer: type-A is designated as having a no flow path directly above the producer and type-B has a flow path directly above the producer. The simulation results show that type-A has a greater impact than type-B on SAGD performance especially for the BIP case. Small shale sizes of 3 and 5 m have a slight impact on performance; however, cases with 10 m shale have a greater impact due to the disruption of gravity drainge to the producer. Type-A BIP may require a longer pre-heating period for successful SAGD operation. Generally, shale barriers of 5 to 25 m are not critical for an AP case regardless of vertical location of shale barriers; however shale barriers greater than 50 m may act as a barrier and reduce the effective pay thickness of the reservoir depending upon the its vertical location.
Molecular Identity of Hematopoietic Precursor Cells Emerging in the Human Embryo (1998)

It is now accepted from studies in animal models that hematopoietic stem cells emerge in the para-aortic mesoderm-derived aorta-gonad-mesonephros region of the vertebrate embryo. We have previously identified the equivalent primitive hematogenous territory in the 4- to 6-week human embryo, under the form of CD34(+)CD45(+)Lin- high proliferative potential hematopoietic cells clustered on the ventral endothelium of the aorta. To characterize molecules involved in initial stem cell emergence, we first investigated the expression in that territory of known early hematopoietic regulators. We herein show that aorta-associated CD34(+) cells coexpress the tal-1/SCL, c-myb, GATA-2, GATA-3, c-kit, and flk-1/KDR genes, as do embryonic and fetal hematopoietic progenitors later present in the liver and bone marrow. Next, CD34(+)CD45(+) aorta-associated cells were sorted by flow cytometry from a 5-week embryo and a cDNA library was constructed therefrom. Differential screening of that library with total cDNA probes obtained from CD34(+) embryonic liver cells allowed the isolation of a kinase-related sequence previously identified in KG-1 cells. In addition to emerging blood stem cells, KG-1 kinase is also strikingly expressed in all developing endothelial cells in the yolk sac and embryo, which suggests its involvement in the genesis of both hematopoietic and vascular cell lineages in humans.
A revision of Hoodia and Lavrania (Asclepiadaceae-Stapelieae) (1994)

Hoodia Sweet ex Decne is revised to contain 13 species which are divided into 2 sections. Sect. Hoodia contains H.currorii, H.dregei, H.gordonii, H.juttae and H.parviflora. Sect. Trichocaulon contains H.alstonii, H.flava, H.mossamedensis, H.officinalis, H.pedicellata, H.pilifera, H.ruschii and H.triebneri, all except H.ruschii formerly constituting the section "Eutrichocaulon", the so-called "spiny" species of Trichocaulon. The remainder of Trichocaulon, the section Cactoidea, is transferred to Lavrania Plowes. This genus then consists of the monotypic section Lavrania (L.haagnerae) and Sect. Cactoidea containing L.cactiformis, L.marlothii, L.perlata and L.picta.
All-trans retinoic acid reverses phorbol ester resistance in a human myeloid leukemia cell line (1994)

Treatment of human HL-60 leukemic cells with 12-O-tetradecanoylphorbol- 13-acetate (TPA) is associated with activation of protein kinase C (PKC) and induction of monocytic differentiation. An HL-60 variant cell line, termed HL-525, derived from long-term exposure to TPA (Homma et al, Proc Natl Acad Sci USA 83: 7316, 1986) is resistant to TPA-induced differentiation and displays decreased PKC beta expression compared with the HL-60 parent line. However, this variant exhibits features of granulocytic differentiation, including nitroblue tetrazolium reduction, when exposed to all-trans retinoic acid (ATRA). Whereas treatment of HL-525 cells with ATRA or TPA alone had no effect on features of monocytic differentiation, these agents in combination resulted in cellular adhesion, nonspecific esterase staining, and induction of the c-fms (monocyte growth factor receptor) gene. In order to measure PKC expression associated with the reversal of TPA resistance by ATRA, we exposed HL-525 cells to ATRA and analyzed PKC- mRNA and protein levels. Exposure of HL-525 cells to ATRA for 3 days resulted in induction of PKC beta transcripts, whereas there was little change in PKC alpha mRNA levels. ATRA treatment was also associated with an increase in PKC activity and an induction of cytosolic PKC beta protein levels. These findings are consistent with the hypothesis that ATRA reverses TPA resistance in HL-525 cells by enhancing the expression of PKC.
Dos and don'ts of client authentication on the web (2001)

Client authentication has been a continuous source of problems on the Web. Although many well-studied techniques exist for authentication, Web sites continue to use extremely weak authentication schemes, especially in non-enterprise environments such as store fronts. These weaknesses often result from careless use of authenticators within Web cookies. Of the twenty-seven sites we investigated, we weakened the client authentication on two systems, gained unauthorized access on eight, and extracted the secret key used to mint authenticators from one. We provide a description of the limitations, requirements, and security models specific to Web client authentication. This includes the introduction of the interrogative adversary, a surprisingly powerful adversary that can adaptively query a Web site. We propose a set of hints for designing a secure client authentication scheme. Using these hints, we present the design and analysis of a simple authentication scheme secure against forgeries by the interrogative adversary. In conjunction with SSL, our scheme is secure against forgeries by the active adversary.
Noggin Expands Neural Stem Cells in the Adult Hippocampus (2008)

New neurons are added to the adult hippocampus throughout life and contribute to cognitive functions, including learning and memory. It remains unclear whether ongoing neurogenesis arises from self-renewing neural stem cells (NSCs) or from multipotential progenitor cells that cannot self-renew in the hippocampus. This is primarily based on observations that neural precursors derived from the subventricular zone (SVZ) can be passaged long term, whereas hippocampal subgranular zone (SGZ) precursors are rapidly depleted by passaging. We demonstrate here that high levels of bone morphogenetic protein (BMP) signaling occur in hippocampal but not SVZ precursors in vitro, and blocking BMP signaling with Noggin is sufficient to foster hippocampal cell self-renewal, proliferation, and multipotentiality using single-cell clonal analysis. Moreover, NSC maintenance requires continual Noggin exposure, which implicates BMPs as crucial regulators of NSC aging. In vivo, Noggin is expressed in the adult dentate gyrus and limits BMP signaling in proliferative cells of the SGZ. Transgenic Noggin overexpression in the SGZ increases multiple precursor cell populations but proportionally increases the glial fibrillary acidic protein-positive cell population at the expense of other precursors, suggesting that Noggin acts on NSCs in vivo. To confirm this, we used a dual thymidine analog paradigm to repeatedly label slowly dividing cells over a long duration. We find that small populations of label-retaining cells exist in the SGZ and that Noggin overexpression increases their numbers. Thus, we propose that the adult hippocampus contains a population of NSCs, which can be expanded both in vitro and in vivo by blocking BMP signaling.
Molecular events in melanoma development and progression (1998)

Based on clinical and histopathological features, five steps of melanoma progression have been proposed: common acquired and congenital nevi with structurally normal melanocytes, dysplastic nevus with structural and architectural atypia, early radial growth phase (RGP) primary melanoma, advanced vertical growth phase primary melanoma (VGP) with competence for metastasis, and metastatic melanoma. Despite a wealth of research resources (tissues, cell lines, and antibodies), the genetic alterations responsible for the development and stepwise progression of melanoma are still unclear. Cytogenetic analyses have failed to identify consistent gene deletions, mutations, translocations, or amplifications in sporadic cases. However, in vitro characterization of melanoma cells has revealed fundamental differences from normal melanocytes. Earlier work using monoclonal antibodies has defined a variety of melanoma-associated antigens that mediate cell-cell or cell-substratum adhesion, growth regulation, proteolysis, and modulation of immune responses. Functional studies of these individual candidate molecules will lead to a better understanding of the pathogenesis of melanoma and of potential targets for rational therapy.
Near‐terminus axonal structure and function following rat sciatic nerve regeneration through a collagen‐GAG matrix in a ten‐millimeter gap (2000)

The objectives of this study were to evaluate the regenerated axon structure at near-terminal locations in the peroneal and tibial branches 1 year following implantation of several tubular devices in a 10-mm gap in the adult rat sciatic nerve and to determine the extent of recovery of selected sensory and motor functions. The devices were collagen and silicone tubes implanted alone or filled with a porous collagen-glycosaminoglycan matrix. Intact contralateral nerves and autografts were used as controls. Nerves were retrieved at 30 and 60 weeks postoperatively for histological evaluation of the number and diameter of regenerated axons proximal and distal to the gap and in the tibial and peroneal nerve branches, near the termination point. Several functional evaluation methods were employed: gait analysis, pinch test, muscle circumference, and response to electrical stimulation. A notable finding was that the matrix-filled collagen tube group had a significantly greater number of large-diameter myelinated axons (≥6 μm in diameter) in the distal nerve branches than any other group, including the autograft group. These results were consistent with previously reported electrophysiological measurements that showed that the action potential amplitude for the A fibers in the matrix-filled collagen tube group was greater than for the autograft control group. Functional testing revealed the existence of both sensory and motor recovery following peripheral nerve regeneration through all devices; however, the tests employed in this study did not show differences among the groups with regeneration. Electrical stimulation in vivo showed that threshold parameters to elicit muscle twitch were the same for reinnervating and control nerves. The investigation is of importance in showing for the first time the superiority of a specific fully resorbable off-the-shelf device over an autograft for bridging gaps in peripheral nerve, with respect to the near-terminus axonal structure. J. Neurosci. Res. 60:666–677, 2000 © 2000 Wiley-Liss, Inc.
Determination of acids and their strength in isobutyl methyl ketone (1982)

The dissociation constants of nitrophenoxazines in isobutyl methyl ketone (MIBK) were determined and correlated with the HNP values in acetone. Of the derivatives studied, the strongest acid is 1,3,7-trinitrophenoxazine (p K = 19.8), the weakest, 1-nitrophenoxazine (p K &gt; 26). The compounds have no tendency to homo- or heteroconjugation, and were used as indicators in determination of weak acids in MIBK. Some derivatives of malonic acid and of 1,2,4-triazine as well as the intermediates used in their synthesis were determined; their HNP and p K values were established. The shape of the potentiometric titration curves can be of assistance in solving some structure problems.
Programmed cell death during heart development. (2002)

Programmed cell death has been demonstrated to be of importance in mammalian organogenesis. In this thesis, the distribution, regulation and function of programmed cell death are investigated during mouse cardiac septation. During this process, the four chambers and two outflow vessels of the heart become separated from one another. In the mouse, this occurs between embryonic days 10.5 to 13.5. The study commences with a detailed spatio-temporal analysis of programmed cell death during cardiac septation. This demonstrates specific, reproducible foci of apoptotic activity, which are grouped into low intensity and high intensity, the latter occurring in the endocardial cushions as septation completes. This qualitative investigation is then supplemented, and supported, by a quantitative analysis. Immunohistochemical techniques demonstrate which cell types undergo apoptosis during cardiac septation and show that macrophages are not clearing apoptotic debris. The question of an association between cardiac neural crest cells and programmed cell death during the process of septation is addressed using double-labelling for a cardiac neural crest marker, [alpha]-smooth muscle actin, and an apoptosis marker, TUNEL, and by investigation of apoptosis in the Sp2H mutant mouse, in which neural crest cell migration to the cardiac outflow tract is impaired. The results suggest that neural crest cells are involved in apoptosis, and may indeed be dying, within the cardiac outflow tract cushions. The molecular mechanisms that lead to programmed cell death in the heart are then examined, focusing on the death receptor-mediated apoptosis pathway. Evidence is provided that this pathway is involved in programmed cell death during septation. Finally, inhibition of apoptosis in embryo culture is described. Although only preliminary, the results suggest that inhibition of programmed cell death can cause defective development of the interventricular septum.
Direction finding algorithms using fourth order statistics: asymptotic performance analysis (1992)

High-resolution direction finding algorithms using higher-order cumulants of the array data is addressed. Two fourth-order cumulant-based matrices are considered: the diagonal cumulant slice and the contracted quadricovariance. They are evaluated in the context of direction of arrival (DOA) estimation using subspace techniques. To this purpose, an original methodology is introduced to derive the closed form of asymptotical performance. This analysis is applied to the cumulant-based DOA estimation problem, establishing on a rational basis the domain of applicability of HOS in DOA estimation, which is larger than usually believed. It is also shown that the contracted quadricovariance outperforms the diagonal slice in all respects. Some numerical evaluations illustrate the results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Phosphorylation determines the binding of microtubule-associated protein 2 (MAP2) to microtubules in living cells. (1991)

The influence of phosphorylation on the binding of microtubule-associated protein 2 (MAP2) to cellular microtubules was studied by microinjecting MAP2 in various phosphorylation states into rat-1 fibroblasts, which lack endogenous MAP2. Conventionally prepared brain MAP2, containing 10 mol of endogenous phosphate per mol (MAP2-P10), was completely bound to cellular microtubules within 2-3 min after injection. MAP2 prepared in the presence of phosphatase inhibitors, containing 25 mol/mol of phosphate (MAP2-P25), also bound completely. However, MAP2 whose phosphate content had been reduced to 2 mol phosphate per mol by treatment with alkaline phosphatase in vitro (MAP2-P2) did not initially bind to microtubules, suggesting that phosphorylation of certain sites in MAP2 is essential for binding to microtubules. MAP2-P10 was further phosphorylated in vitro via an endogenously bound protein kinase activity, adding 12 more phosphates, giving a total of 22 mol/mol. This preparation (MAP2-P10+12) also did not bind to microtubules. Assay of the binding of these preparations to taxol-stabilized tubulin polymers in vitro confirmed that their binding to tubulin depended on the state of phosphorylation, but the results obtained in microinjection experiments differed in some cases from in vitro binding. The results suggest that the site of phosphate incorporation rather than the amount is the critical factor in determining microtubule binding activity of MAP2. Furthermore, the interaction of MAP2 with cellular microtubules may be influenced by additional factors that are not evident in vitro.
Susceptibility of the mammary gland to carcinogenesis: I Differentiation of the mammary gland as determinant of tumor incidence and type of lesion. (1979)

The influence of age and mammary gland differentiation on the incidence of tumors induced by 7,12-dimethylbenz(a)anthracene (DMBA) was studied by correlating the development of the mammary glands of 20-180-day-old, virgin Sprague-Dawley rats with the number and type of tumors induced by DMBA administered at those various ages. The number of terminal end buds (TEBs), terminal ducts (TDs), and alveolar buds (ABs)/sq mm and their DNA-labeling indices (DNA-LI) were determined. Highest density of TEB occurred when the rats were 20 days old, decreasing thereafter. DNA-LI ranged between 25.2 and 29 in TEB of rats aged 30-55 days, which was coincident with the highest incidence of carcinomas. With aging, the number of TEBs and their DNA-LI decreased and the number of TDs and ABs increased, although with a low DNA-LI, which correlated with a lower incidence of carcinomas and higher incidence of benign lesions.
Alterations in the internucleosomal DNA helical twist in chromatin of human erythroleukemia cells in vivo influences the chromatin higher‐order folding (1995)

In the present study chloroquine diphosphate, a DNA intercalating drug, was used to alter the internucleosomal DNA helical twist in chromatin of living mammalian cells. The intercalative binding of chloroquine effectively unwinds the DNA double helix and its binding is restricted to nucleosomal linker regions without noticeable disruption of nucleosomes. The results presented here imply that the alterations in the rotation angle between the adjacent nucleosomes in chromatin of eukaryotic cells in vivo significantly influences the way the chain of nucleosomes folds in higher-order chromatin structures, as evidenced by specific alterations in nuclease susceptibility of chromatin.
802.11 Wireless Networks: The Definitive Guide (2002)

As we all know by now, wireless networks offer many advantages over fixed (or wired) networks. Foremost on that list is mobility, since going wireless frees you from the tether of an Ethernet cable at a desk. But that's just the tip of the cable-free iceberg. Wireless networks are also more flexible, faster and easier for you to use, and more affordable to deploy and maintain. The de facto standard for wireless networking is the 802.11 protocol, which includes Wi-Fi (the wireless standard known as 802.11b) and its faster cousin, 802.11g. With easy-to-install 802.11 network hardware avail