gebhart/patrepeval huggingface dataset:
Targeting the tumor microenvironment with chemically modified tetracyclines: inhibition of laminin 5 gamma2 chain promigratory fragments and vasculogenic mimicry. (2002)

The laminin 5 (Ln-5) gamma2 chain and matrix metalloproteinases (MMPs) MMP-2 and membrane type 1 (MT1)-MMP act cooperatively and are required for highly aggressive melanoma cells to engage in vasculogenic mimicry when cultured on a three-dimensional matrix. Furthermore, generation of Ln-5 gamma2 chain promigratory fragments by MMP-2 and MT1-MMP proteolysis is necessary for an aggressive tumor cell-preconditioned matrix to induce vasculogenic mimicry in poorly aggressive tumor cells. These observations suggest that treatment regimes that specifically target aggressive tumor cells may fail to take into account changes in the extracellular microenvironment that persist after removal or destruction of an aggressive tumor and could result in a recurrence or continuance of the tumor. As a potential therapeutic approach to address this concern, the work presented here measured the molecular consequences of adding a chemically modified tetracycline (CMT-3; COL-3) that inhibits MMP activity to aggressive metastatic melanoma cells in three-dimensional culture. COL-3 inhibited vasculogenic mimicry and the expression of vasculogenic mimicry-associated genes in aggressive cells, as well as the induction of vasculogenic mimicry in poorly aggressive cells seeded onto an aggressive cell-preconditioned matrix. Furthermore, molecular analysis revealed that COL-3 not only inhibited the generation of Ln-5 gamma2 chain promigratory fragments in the aggressive cell-preconditioned matrix but also inhibited the induction of Ln-5 gamma2 chain gene expression in poorly aggressive cells by the aggressive cell-preconditioned matrix. These results suggest that COL-3 (and related chemically modified tetracyclines) may be useful in targeting molecular cues in the microenvironment of aggressive tumors and could potentially be used in a combinatorial manner with other therapies that specifically target and kill aggressive tumor cells.
The generalized trace-norm and its application to structure-from-motion problems (2011)

In geometric computer vision, the structure from motion (SfM) problem can be formulated as a optimization problem with a rank constraint. It is well known that the trace norm of a matrix can act as a convex proxy for a low rank constraint. Hence, in recent work [7], the trace-norm relaxation has been applied to the SfM problem. However, SfM problems often exhibit a certain structure, for example a smooth camera path. Unfortunately, the trace norm relaxation can not make use of this additional structure. This observation motivates the main contribution of this paper. We present the so-called generalized trace norm which allows to encode prior knowledge about a specific problem into a convex regularization term which enforces a low rank solution while at the same time taking the problem structure into account. While deriving the generalized trace norm and stating its different formulations, we draw interesting connections to other fields, most importantly to the field of compressive sensing. Even though the generalized trace norm is a very general concept with a wide area of potential applications we are ultimately interested in applying it to SfM problems. Therefore, we also present an efficient algorithm to optimize the resulting generalized trace norm regularized optimization problems. Results show that the generalized trace norm indeed achieves its goals in providing a problem-dependent regularization.
In ovo time-lapse analysis after dorsal neural tube ablation shows rerouting of chick hindbrain neural crest (2000)

Previous analyses of single neural crest cell trajectories have suggested important roles for interactions between neural crest cells and the environment, and amongst neural crest cells. To test the relative contribution of intrinsic versus extrinsic information in guiding cells to their appropriate sites, we ablated subpopulations of premigratory chick hindbrain neural crest and followed the remaining neural crest cells over time using a new in ovo imaging technique. Neural crest cell migratory behaviors are dramatically different in ablated compared with unoperated embryos. Deviations from normal migration appear either shortly after cells emerge from the neural tube or en route to the branchial arches, areas where cell-cell interactions typically occur between neural crest cells in normal embryos. Unlike the persistent, directed trajectories in normal embryos, neural crest cells frequently change direction and move somewhat chaotically after ablation. In addition, the migration of neural crest cells in collective chains, commonly observed in normal embryos, was severely disrupted. Hindbrain neural crest cells have the capacity to reroute their migratory pathways and thus compensate for missing neural crest cells after ablation of neighboring populations. Because the alterations in neural crest cell migration are most dramatic in regions that would normally foster cell-cell interactions, the trajectories reported here argue that cell-cell interactions have a key role in the shaping of the neural crest migration.
A batch of PNUTS (2011)

Cloud data management systems are growing in prominence, particularly at large Internet companies like Google, Yahoo!, and Amazon, which prize them for their scalability and elasticity. Each of these systems trades off between low-latency serving performance and batch processing throughput. In this paper, we discuss our experience running batch-oriented Hadoop on top of Yahoo's serving-oriented PNUTS system instead of the standard HDFS file system. Though PNUTS is optimized for and primarily used for serving, a number of applications at Yahoo! must run batch-oriented jobs that read or write data that is stored in PNUTS.
Glycans and glycosylation of platelets: current concepts and implications for transfusion (2008)

Room temperature storage of platelet products increases the risk of transfusion-mediated sepsis and accelerates platelet deterioration, limiting platelet shelf life. Recent evidence suggests that glycoengineering of platelets might allow for their cold storage, significantly improving the quality of platelet products.
Effect of pre- and post-treatment with Ashwagandha i-Extract on scopolamine-induced changes in BDNF and GFAP expression in mice brain. (2015)

&lt;p&gt;Effects of pre, post and &lt;i&gt;per se&lt;/i&gt; treatment of i-Extract (200 mg/Kg BW) on mRNA expression (A) and protein (B) levels of BDNF and GFAP in the mouse cerebrum. Data was quantitated and is presented as percent relative units. Lane 1-Control, Lane 2-scopolamine, Lane 3-post-treatment with i-Extract, Lane 4-&lt;i&gt;per se&lt;/i&gt; treatment of i-Extract, Lane 5-Pre-treatment with i-Extract. *denotes significant differences (P&lt;0.05) between the SC group and i-Extract group. #denotes significant differences (P&lt;0.05) between Control and SC group.&lt;/p&gt;
Inactivated Seasonal Influenza Vaccines Increase Serum Antibodies to the Neuraminidase of Pandemic Influenza A(H1N1) 2009 Virus in an Age‐Dependent Manner (2010)

Levels of preexisting antibodies to the hemagglutinin of pandemic influenza A(H1N1) 2009 (hereafter pandemic H1N1) virus positively correlate with age. The impact of contemporary seasonal influenza vaccines on establishing immunity to other pandemic H1N1 proteins is unknown. We measured serum antibodies to the neuraminidase (NA) of pandemic H1N1 in adults prior to and after vaccination with seasonal trivalent inactivated influenza vaccines. Serum antibodies to pandemic H1N1 NA were observed in all age groups; however, vaccination elevated levels of pandemic H1N1 NA antibodies predominately in elderly individuals (age, ⩾60 years). Therefore, contemporary seasonal vaccines likely contribute to reduction of pandemic H1N1-associated disease in older individuals.
Vegetable Tannins and Dyestuffs (2018)

The use of vegetable tannins and dyes is unquestionably as old as civilisation itself, having been used for preparing leather from animal hides and skins and for colouring purposes, respectively. The art of tanning and dyeing seems to have developed independently by the people of both the Old and the New Worlds using different materials and methods. The vegetable dyes have lost ground largely to the synthetics, such as alizarin or aniline dyes obtained from once ‘useless’ coal tar substances. Only a small fraction of the dyes used today is of natural origin. Those who still use vegetable dyes, however, believe that no synthetic dye has a comparable lustre, the underglow of rich colour or the soft light and shadow so appealing to the eye. They consider synthetic dyes as garish and harsh. Vegetable tannins, on the other hand, have retained their prominence and are still in great demand since, the synthetic products (syntans) could not be made available at competitive prices. Although nowadays, more and more mineral tannins, inorganic salts (such as those of chromium and zirconium) and other tanning agents are being used. In addition, the demand for leather substitutes, such as synthetic leather and composition shoe soles is steadily increasing. Most of the synthetic and mineral tannins now in use lack certain attributes necessary to obtain heavy leather and, therefore, cannot be considered as true substitutes for vegetable tannins. Nonetheless, vegetable tannins are still sufficiently important to merit some discussion whereas the vegetable dyes are treated for nothing more than their historical importance.
Supplementary Figures 1-13 from A Squalene-Based Nanomedicine for Oral Treatment of Colon Cancer (2023)

&lt;p&gt;Supplementary Figure 1 shows the viability of cancer cell lines treated with drugs. Supplementary Figure 2 demonstrates the cytotoxicity of CDDP and SQ-CDDP NP on primary culture of mice rectal tumors. Supplementary Figure 3 illustrates the relative mRNA expression levels of CTR1, CCS, ATP7A, ATP7B, MRP2, GSTP1 and MT2A involved in CDDP influx/efflux, intracellular trafficking and detoxification in a series of human carcinoma cell lines. Supplementary Figure 4 shows the contribution of CTR1 influx transporter and the copper transporter ATP7A in the cellular accumulation of CDDP or SQ-CDDP NP. Supplementary Figure 5 shows the comparative effects of SQ-CCDP NP and CDDP on the effectors systems involved in CDDP resistance of the colonic KM-12 cancer cells. Supplementary Figure 6 and 7 show the stability of SQ-CDDP NP and drug release in simulated digestive fluids and pharmacokinetic analysis of platinum. Supplementary Figure 8 shows the overall toxicity of CDDP and SQ-CCDP NP administered orally in mice. Supplementary Figure 9 shows the relative tissue platinum biodistribution. Supplementary Figure 10 shows the toxicity of CDDP and SQ-CCDP NP on colonic epithelial cells in vivo. Supplementary Figure 11 shows the anticancer efficacy of orally administered SQ-CCDP NP versus CDDP injected iv on the development of colonic tumors induced by AOM/DSS in Balb/c mice. Supplementary Figure 12 shows the tissue distribution of platinum after multiple oral administration of CDDP and SQ-CDDP NP to Balb/c mice. Supplementary Figure 13 shows the inhibition of liver and lymph nodes metastasis in intracecal orthotopic graft in nude mice.&lt;/p&gt;
PROD: A VLSI Fault Diagnosis System (1985)

Faults in the manufacturing of VLSI chips lower the effective yield, thus increasing manufacturing cost. Early diagnosis of faults can avoid this sitution. Such diagnoses can be made by PROD, a diagnostic expert system that analyzes the joint probability density function of measured IC parameters density fuction of measured IC parameters to determine the source of faults resulting in faults chips. PROD can identify both parametric and catastrophic faults, and the expert system can be expanded to diagnose faults that cannot be described quantitatively. This article describes PROD's diagnostic algorithms and their implementation in the complete diagnostic system, and includes several exmples that illustrate its capabilities.
Suicidal Behavior During Lithium and Valproate Treatment: A Within-Individual 8-Year Prospective Study of 50,000 Patients With Bipolar Disorder (2017)

The results suggest that lithium should be considered for patients with bipolar disorder with suspected suicidal intentions, although risk for suicide is only one of the considerations when providing clinical care.
A model and methodology for hardware-software codesign (1993)

A behavioral model of a class of mixed hardware-software systems is presented. A codesign methodology for such systems is defined. The methodology includes hardware-software partitioning, behavioral synthesis, software compilation, and demonstration on a testbed consisting of a commercial central processing unit (CPU), field-programmable gate arrays, and programmable interconnections. Design examples that illustrate how certain characteristics of system behavior and constraints suggest hardware or software implementation are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Asymmetric Zipper-Coupled Tubes and Smooth Sheet Attachments in the Design of Deployable Space-Filling Mechanisms (2023)

Abstract Zipper-coupled tubes are a unique structure consisting of two tubes with zig-zag walls that, when coupled in a zipper fashion, resist compression in the normal direction. A wider application of zipper-coupled tubes, however, is precluded by their angular form. By focusing on a subset of zipper-coupled tubes with parallel and coplanar creases constructed by repeating asymmetric degree-four vertex cells, we design a smooth sheet attachment that lies flat when the asymmetric zipper-coupled tubes are fully deployed, increasing the utility of the otherwise jagged tubes. Furthermore, we provide an explicit mathematical model of the motion of the resulting mechanism, thereby demonstrating its rigid-foldability.
Observation of a π- to σ-rearrangement upon proton addition to bicyclo[6,1,0]nonatrienetricarbonylmolybdenum (1973)

Proton addition to bicyclo[6,1,0]nonatrienetricarbonylmolybdenum (I) gives complex (II) in which a π- to σ-rearrangement has taken place with σ-bonding between Mo and C(2) and π-bonding between Mo and the pentadienyl C(3)–C(7).
Divergence(s) in nodal signaling between aggressive melanoma and embryonic stem cells (2014)

The significant role of the embryonic morphogen Nodal in maintaining the pluripotency of embryonic stem cells is well documented. Interestingly, the recent discovery of Nodal's re-expression in several aggressive and metastatic cancers has highlighted its critical role in self renewal and maintenance of the stem cell-like characteristics of tumor cells, such as melanoma. However, the key TGFβ/Nodal signaling component(s) governing Nodal's effects in metastatic melanoma remain mostly unknown. By employing receptor profiling at the mRNA and protein level(s), we made the novel discovery that embryonic stem cells and metastatic melanoma cells share a similar repertoire of Type I serine/threonine kinase receptors, but diverge in their Type II receptor expression. Ligand:receptor crosslinking and native gel binding assays indicate that metastatic melanoma cells employ the heterodimeric TGFβ receptor I/TGFβ receptor II (TGFβRI/TGFβRII) for signal transduction, whereas embryonic stem cells use the Activin receptors I and II (ACTRI/ACTRII). This unexpected receptor usage by tumor cells was tested by: neutralizing antibody to block its function; and transfecting the dominant negative receptor to compete with the endogenous receptor for ligand binding. Furthermore, a direct biological role for TGFβRII was found to underlie vasculogenic mimicry (VM), an endothelial phenotype contributing to vascular perfusion and associated with the functional plasticity of aggressive melanoma. Collectively, these findings reveal the divergence in Nodal signaling between embryonic stem cells and metastatic melanoma that can impact new therapeutic strategies targeting the re-emergence of embryonic pathways.
Quantized fracture mechanics and related applications for predicting the strength of defective nanotubes (2004)

A new energy-based theory, Quantized Fracture Mechanics (QFM), is presented that modifies continuum-based fracture mechanics. The differentials in Griffith’s criterion are substituted with finite differences; the implications are remarkable. Fracture of tiny systems with a given geometry and type of loading occurs at quantized stresses that are well predicted by QFM. QFM is self-consistent, agreeing to first-order with linear elastic fracture mechanics (LEFM), and to second-order with non-linear fracture mechanics (NLFM): the equation of the R-curve is consequently derived. For vanishing crack length QFM predicts a finite ideal strength in agreement with Orowan’s prediction. The different fracture Modes (opening I, sliding II and tearing III), and the stability of the fracture propagations, are treated in a simple way. In contrast to LEFM, QFM has no restrictions on treating defect size and shape. As an example, strengths predicted by QFM are compared with experimental and numerical results on carbon nanotubes containing defects of different size and shape.
ReaxFF Simulations of Lignin Fragmentation on a Palladium-Based Heterogeneous Catalyst in Methanol–Water Solution (2018)

The interaction of fragments derived from lignin depolymerization with a heterogeneous palladium catalyst in methanol-water solution is studied by means of experimental and theoretical methodologies. Quantum chemistry calculations and molecular dynamics simulations based on the ReaxFF approach are combined effectively to obtain an atomic level characterization of the crucial steps of the adsorption of the molecules on the catalyst, their fragmentation, reactions, and desorption. The main products are identified, and the most important routes to obtain them are explained through extensive computational procedures. The simulation results are in excellent agreement with the experiments and suggest that the mechanisms comprise a fast chemisorption of identified fragments from lignin on the metal interface accompanied by bond breaking, release of some of their hydrogens and oxygens to the support, and eventual desorption depending on the local environment. The strongest connections are those involving the aromatic rings, as confirmed by the binding energies of selected representative structures, estimated at the quantum chemistry level. The satisfactory agreement with the literature, quantum chemistry data, and experiments confirms the reliability of the multilevel computational procedure to study complex reaction mixtures and its potential application in the design of high-performance catalytic devices.
ChemInform Abstract: Anionic Hetero(3,3)Rearrangements. N‐Acyl‐N′‐enylhydrazines to Pyrrolidinones. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Therapy-related acute myeloid leukemia and myelodysplastic syndromes in patients with Hodgkin lymphoma: a report from the German Hodgkin Study Group Short title: t-AML/MDS after Hodgkin lymphoma (2017)

Therapy-related acute myeloid leukemia and myelodysplastic syndromes (tAML/MDS) represent severe late effects in patients treated for Hodgkin lymphoma (HL). As more recent data are scarce, we retrospectively analyzed incidence, outcome and risk factors for the development of t-AML/MDS after HL. A total of 11952 patients treated for newly diagnosed HL within GHSG trials between 1993 and 2009 were considered. At a median follow-up of 72 months, t-AML/MDS was diagnosed in 106/11952 patients (0.9%). Median time from HL treatment to tAML/MDS was 31 months. The median age of patients with t-AML/MDS was higher than in the whole patient group (43 vs 34 years, p<0.0001). Patients who received four or more cycles of BEACOPPescalated had an increased risk to develop t-AML/MDS when compared with patients treated with less than four cycles of BEACOPPescalated or no BEACOPP chemotherapy (1.7% vs 0.7% vs 0.3%, p<0.0001). The median OS for all t-AML/MDS patients was 7.2 months. However, t-AML/MDS patients proceeding to allogeneic stem cell transplantation (aSCT) had a significantly better outcome with a median OS not reached after a median follow-up of 41 months (p<0.001). For personal use only. on February 3, 2017. by guest www.bloodjournal.org From
Supplementary Figure 4 from Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity (2023)

&lt;p&gt;Increased CXCL12 within tumor cells by RNA in situ hybridization following cabozantinib treatment.&lt;/p&gt;
ChemInform Abstract: Synthesis of Pseudo‐oligosaccharidic Glycosidase Inhibitors. Part 3. (1986)

Abstract Die Kondensation der Aminozucker (I) mit den Epoxiden (II) bzw. (V) führt zu chromatographisch trennbaren Diastereomerengemischen der im Titel genannten Pseudodisaccharide (III) und (IV) bzw. (VI) und (VII).
Spread-Spectrum Multiple-Access Performance of Orthogonal Codes: Linear Receivers (1987)

This paper analyzes a direct-sequence, spread-spectrum, multiple-access (SSMA) communication system which assigns a set of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</tex> orthogonal sequences to each user. With all direct sequence SSMA systems, <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</tex> users share a channel by phase modulating their transmissions with signature sequences. However, the users of our system transmit <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">log_{2}M</tex> bits of information/sequence. This contrasts classical SSMA schemes which use a pair of antipodal sequences and transmit 1 bit/sequence. In this paper, we assume that the channel noise is a combination of additive white Gaussian noise (AWGN) and multiple-access interference. We employ the optimum (single-user) demodulator for orthogonal signals in Gaussian noise. The multiple-user performance of this receiver is analyzed. We obtain approximations for the multiuser probability of error by using a Gaussian approximation for the multiple-access interference. We also obtain an upper bound on the exact probability by using characteristic functions. Our SSMA system is Well suited for application at the lower radio frequencies. Therefore, a companion paper describes a realistic model for low-frequency radio noise, modifies the receiver to include a zero-memory nonlinearity, and studies the performance of the nonlinear receiver.