gebhart/patrepeval huggingface dataset:
103 TIMP expression in Patellar tendon IS affected by Surgical menopause (2014)

<h3>Introduction</h3> Degenerative changes in tendinopathy may be related to imbalance of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) [Jones, 2006]. The rate of human Achilles tendon rupture in women was noted to start to increase after menopause [Maffulli, 1999]. This study examines the effect of surgical menopause on rabbit patellar tendons (PTs) comparing molecular expression of MMPs and TIMPs. We hypothesised that PTs from rabbits following ovariohysterectomy (OVH) surgery would have increased MMP expression and decreased TIMP expression compared with PTs from intact normal rabbits. <h3>Methods</h3> PTs from three groups of female New Zealand White rabbits were evaluated: intact normal (n = 8; 1-year-old), adult OVH (n = 8, 14 weeks post-OVH surgery at 1-year-old), adolescent OVH (n = 9, 33 weeks post-OVH surgery at 15-weeks-old). PTs underwent RT-qPCR with rabbit specific primers for MMPs (MMP-1, MMP-3, MMP-13) and TIMPs (TIMP-1, TIMP-2, TIMP-3), and the housekeeping gene 18S. Data were compared using Kruskal-Wallis tests with Conover post-hoc analyses. <h3>Results</h3> The expression of TIMP-2 was decreased in PTs from adult OVH rabbits and adolescent OVH rabbits compared with PTs from intact normal rabbits (p &lt; 0.05; Figure 1). The expression of TIMP-3 was decreased in PTs from adolescent OVH rabbits compared with PTs from intact normal rabbits (p &lt; 0.05; Figure 2). TIMP-3 expression was decreased in PTs from adolescent OVH rabbits compared with adult OVH rabbits (p &lt; 0.05; Figure 2). The expressions of MMP-1, MMP-3, MMP-13 and TIMP-1 were not statistically different when comparing PTs from the three groups. <h3>Discussion</h3> TIMP-2 expression in patellar tendon was decreased following surgical menopause in adult and adolescent rabbits and TIMP-3 expression in patellar tendon was decreased following surgical menopause in adolescent rabbits, with no changes in the other TIMPs and MMPs investigated. These findings suggest an MMP/TIMP expression imbalance towards degradation in tendon with loss of oestrogen. Although TIMP-2 and TIMP-3 expression were not changed in human degenerated patellar tendons [Parkinson, 2010] compared with normal tendons, TIMP-3 expression was decreased in human degenerated Achilles tendons [Jones, 2006] and TIMP-2 and TIMP-3 expression were decreased in human ruptured Achilles tendons [Jones, 2006] and human ruptured rotator cuff tendons [Lo, 2004] compared with normal tendons. <h3>Acknowledgements</h3> NSERC, CIHR <h3>References</h3> Jones <i>et al</i>. Arthritis Rheum. 2006;54:832–842 Maffulli <i>et al</i>. Clin J Sport Med. 1999;9:157–160 Parkinson <i>et al</i>. Arthritis Rheum. 2010;62:3028–3035 Lo <i>et al</i>. Am J Sports Med. 2004;32:1223–1229
Quantum Proteolytic Activation of Chemokine CCL15 by Neutrophil Granulocytes Modulates Mononuclear Cell Adhesiveness (2005)

Monocyte infiltration into inflammatory sites is generally preceded by neutrophils. We show here that neutrophils may support this process by activation of CCL15, a human chemokine circulating in blood plasma. Neutrophils were found to release CCL15 proteolytic activity in the course of hemofiltration of blood from renal insufficiency patients. Processing of CCL15 immunoreactivity (IR) in the pericellular space is suggested by a lack of proteolytic activity in blood and blood filtrate, but a shift of the retention time (t(R)) of CCL15-IR, detected by chromatographic separation of CCL15-IR in blood and hemofiltrate. CCL15 molecules with N-terminal deletions of 23 (delta23) and 26 (delta26) aa were identified as main proteolytic products in hemofiltrate. Neutrophil cathepsin G was identified as the principal protease to produce delta23 and delta26 CCL15. Also, elastase displays CCL15 proteolytic activity and produces a delta21 isoform. Compared with full-length CCL15, delta23 and delta26 isoforms displayed a significantly increased potency to induce calcium fluxes and chemotactic activity on monocytes and to induce adhesiveness of mononuclear cells to fibronectin. Thus, our findings indicate that activation of monocytes by neutrophils is at least in part induced by quantum proteolytic processing of circulating or endothelium-bound CCL15 by neutrophil cathepsin G.
Bounds on the throughput of congestion controllers in the presence of feedback delay (2003)

We consider decentralized congestion control algorithms for low-loss operation of the Internet using the ECN bit. There has been much analysis of such algorithms, but with a few exceptions, these typically ignore the effect of feedback delays in the network on stability. We study a single node with many flows passing through it, with each flow (possibly) having a different round-trip delay. Using a fluid model for the flows, we show that even with delays, the total data rate at the router is bounded; and this bound shows that the (peak) total rate grows linearly with increase in system size, i.e., the fraction of overprovisioning required is constant with respect to N, the number of flows in the system. Further, for typical user data rates and delays seen in the Internet today, the bound is very close to the data rate at the router without delays. Earlier results by Johari and Tan have given conditions for a linearized model of the network to be (locally) stable. We show that even when the linearized model is not stable, the nonlinear model is upper bounded, i.e., the total rate at the bottleneck link is upper bounded, and the upper bound is close to the equilibrium rate for TCP.
Abstract 3120: MMP-7 increases migration by decreasing intercellular cell junction complexes in prostate cancer microtumors formed by perlecan/HSPG2 (2021)

Abstract Background: Polarized epithelium is stabilized by lateral cell-cell interactions via cell adhesion molecules (CAMs) and by cell-matrix interactions with basement membrane including with perlecan/HSPG2 (pln). Prostate cancer (PCa) patients with bone metastases have circulating pln fragments, with inverse correlation between MMP-7 staining and loss of pln in cancer tissue. Cleavage of pln by MMP-7 increases cell-matrix interactions and dysregulates cell signaling, permitting migration. We earlier showed pln domain IV-3 (DmIV-3) drives cell-cell cohesion and, when digested with MMP-7, drives cell dyscohesion. Methods: To evaluate the impact of MMP-7 and pln fragments on microtumor dyscohesion and cell migration, uniformly sized PCa microtumors were pre-formed in a microwell system. Pre-formed microtumors were transferred to Dm IV-3 or full length perlecan (FL pln) coated wells for 16-24 hrs. Microtumors were treated with MMP-7 alone or MMP-7 plus predigested Dm IV-3 fragments or MMP-7 plus FL pln fragments. For live cell imaging, tracking of migratory cells leaving microtumors was performed with Imaris software. Co-location of cell adhesion complex components was assessed with Imaris Spots. Results: Pre-formed microtumors cultured with DmIV-3 cleaved by MMP-7 showed lower Pearson's correlation values at cell boundaries compared to microtumors treated with intact Dm IV-3. Line scan analysis revealed E-cadherin and F-actin fluorescent signals were enriched and co-aligned in microtumors treated with Dm IV-3; enrichment and co-alignment were reduced when DmIV-3 fragments and MMP-7 were present. Track number detected per cell cluster was highest in the presence of FL pln fragments plus MMP-7 along with a measurable change in distribution of track displacement lengths of cells toward high values. Conclusion: Boundary reorganization promotes a migratory cell phenotype in microtumors treated with MMP-7 and DmIV-3 fragments. DmIV-3 fragments generated by MMP-7 cleavage can enhance cell dyscohesion by disrupting interactions between CAMs. Ongoing work will identify DmIV-3 fragment(s) positively associated with tumor dyscohesion that play key roles in secondary metastasis formation. Following patterns of dyscohesion of pre-formed microtumors provides a good model to study dynamic changes in intercellular junction components and quantitate cell migration patterns that foster circulating tumor cell formation and metastasis. Citation Format: Lissette A. Cruz, Tristen V. Tellman, Oleg Igoshin, Daniel Carson, Mary (Cindy) Farach-Carson. MMP-7 increases migration by decreasing intercellular cell junction complexes in prostate cancer microtumors formed by perlecan/HSPG2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3120.
Climate of a cave laboratory representative for rock art caves in the Vézère area (south-west France) (2023)

Leye Cave (Dordogne, France) is a laboratory cave in the Vézère area, a region that contains some of the most famous rock art caves in the world such as Lascaux, Font-de-Gaume and Combarelles, and is listed as Human World Heritage by UNESCO. Leye Cave was selected because it is representative of painted caves, with respect to parameters such as its geological stage, the presence of water and carbon dioxide, the geological state of its walls, and the size of the cave. These wall states are studied to better understand the conditions of conservation of rock art caves without damaging them. The choice of an equivalent medium, i.e., a non-painted cave, was made to be able to conduct experiments or take measurements that would not have been possible in a rock art cave. The climatic conditions (temperature, hygrometry, etc.) monitored since 2011 are central to our understanding of the genesis and evolution of wall states. Leye Cave is sub-horizontal then descendant, forming a cold air trap. The phenomenon of condensation is thought to be important in the genesis of these wall states. Our article presents a model which describes the competition that exists between the conduction of the rock heating the air and the convection cooling the rock, in the area named the “Throne Chamber”, located in the deepest parts of the cave.
Analytical Constructions of a Family of Dense Tetrahedron Packings and the Role of Symmetry (2009)

The determination of the densest packings of regular tetrahedra (one of the five Platonic solids) is attracting great attention as evidenced by the rapid pace at which packing records are being broken and the fascinating packing structures that have emerged. We have discovered the densest known packings of regular tetrahedra with a density $ϕ= {12250/14319} = 0.855506...$. These packings are special cases of an analytical two-parameter family of dense periodic packings with four particles per fundamental cell that we have constructed here. From this family, we can recover a set of recent packing arrangements due to Kallus {\it et al.} [arXiv:0910.5226] with density $ϕ={100/117}=0.854700...$, which has higher symmetry than our densest packings, We also describe a procedure that could lead to rigorous upper bounds on the maximal density of tetrahedron packings, which could aid in assessing the packing efficiency of candidate dense packings.
Fe3O4/chitosan nanocomposite for magnetic drug targeting to cancer (2012)

Magnetic nanoparticles have been introduced in the cancer arena to optimize the accumulation of the drug dose into the tumor interstitium by means of a magnetic gradient. As a result, the chemotherapeutic agent may exhibit an enhanced anticancer efficacy and a negligible systemic toxicity. In these contexts, we have used the coacervation methodology for the design of magnetite/chitosan (core/shell) nanocomposites. The heterogeneous structure of these multifunctional nanoparticles allows the possibility of their use in drug delivery thanks to their excellent responsiveness to magnetic gradients. A detailed characterization of these nanocomposites (including electron microscopy observations, infrared spectrometry, electrophoresis, and thermodynamic analysis) suggested a complete polymeric coverage of the magnetite nuclei. The magnetic responsiveness of the magnetite/chitosan nanoparticles was quantitatively investigated by the hysteresis cycle and qualitatively confirmed by microscopic visualization of the performance of the nanocomposite suspensions under exposure to a 1.1 T permanent magnet. This nanodevice has been used to enhance the intravenous delivery of the anticancer agent gemcitabine to the cancer tissue. Compared to the surface adsorption technique, gemcitabine entrapment into the polymeric shell yielded higher drug loading values, and a slower drug release profile. Heating characteristics of the nanocomposites have been investigated in a high frequency alternating magnetic gradient: a stable maximum temperature of 45 °C was successfully achieved within 30 min. Finally, an in vivo proof of concept using Prussian blue staining has further confirmed the magnetic targeting capabilities of this magnetite/chitosan core/shell nanodevice. Thus, the here described stimuli-sensitive nanomedicine possesses important characteristics, such as magnetically targeted drug delivery, high drug loading and low burst release, as well as hyperthermia inducing capability, indicating its potential for effective therapy of cancer.
Differentiation requires continuous regulation. (1991)

Article de synthese traitant des mecanismes biochimiques et genetiques regulant le phenomene de differenciation cellulaire pour 2 especes d'insectes presentant ou non des mutations dans leur genome
Sex Differences in Efficacy of Pharmacological Therapies in Heart Failure with Reduced Ejection Fraction: A Meta-Analysis (2022)

Our meta-analysis showed no differences between sex in treatment effect for BB and RASi. Review on previously published trials for MRA, SGLT2i, and emerging therapies presented consistent treatment effects between men and women.
Selective F or Br Functionalization of Dibenzofuran for Application as Host Materials of Phosphorescent Organic Light‐Emitting Diodes (2017)

Four dibenzofuran-type host materials substituted with a carbazolylcarbazole moiety were synthesized to investigate the effect of substitution position on the material parameters and device performances of host materials. The carbazolylcarbazole moiety was substituted at the 1-, 2-, 3-, and 4-positions of dibenzofuran by F or Br for a comprehensive study of the positional effect of dibenzofuran-derived host materials. Systematic synthesis and comparison of the four host materials revealed that 1-, 2-, and 4-position modification was better than 3-position modification for high triplet energy and high external quantum efficiency.
On the Validity of the Likelihood Ratio Test and Consistency of Resulting Parameter Estimates in Joint Linkage and Linkage Disequilibrium Analysis under Improperly Specified Parametric Models (2011)

It has been shown that parametric analysis of linkage disequilibrium conditional on linkage using an overly deterministic model can be optimal for family-based association analysis. However, if one applies this strategy carelessly, there is a risk of false inference. We analyse properties of such likelihood ratio tests when the assumed disease mode of inheritance is inaccurate. Under some conditions, problems result if one is not careful to consider what null hypothesis is being tested. We show that: (a) tests for which the null hypothesis assumes the absence of both linkage and association are independent of the true mode of inheritance; (b) likelihood ratio tests assuming either linkage or association under the null hypothesis may depend on the true mode of inheritance, leading to inconsistent parameter estimates, in particular under extremely deterministic models; (c) this problem cannot be eliminated by increasing sample size or adding population controls--as sample size increases, the chance of false positive inference goes to 100%; (d) this issue can lead to systematic false positive inference of association in regions of linkage. This is important because highly deterministic models are often used intentionally in model-based analyses because they can have more power than the true model, and are implicit in many model-free analysis methods.
2-methylbutyryl-CoA dehydrogenase deficiency associated with autism and mental retardation: a case report (2007)

This mutation was also found in two previously reported cases with SBCADD, both originating from Somalia and Eritrea, indicating that it is relatively prevalent in this population. Autism has not previously been described with mutations in this gene, thus expanding the clinical spectrum of SBCADD.
Silicon-Wafer Cleaning with Aqueous Surfactant-Stabilized Gas/Solids Suspensions (2010)

As feature sizes in the microelectronics industry diminish, cleanliness becomes an ever more important requirement. In response to these challenges, a novel wet-cleaning technology was developed at Lam Research Corporation to remove strongly adhered contaminants. An alkaline, foamed aqueous dispersion of insoluble platelet solids flows in linear shear past a particle-contaminated surface. Contaminant removal increases with solids concentration, foam quality, process time, and shear rate and can approach 100%. Particle-removal experiments indicate that dispersed solids are necessary for contaminant removal. Exponential decline of adhered particles with number of immersion/withdrawal events and a linear increase in the rate of particle removal with solids concentration indicate that the removal mechanism is binary collision between the insoluble fatty-acid platelets and contaminant particles. Foam or surfactant solution alone is not effective in particle removal. A binary-collision rate model is derived to relate particle detachment to contact time. The binary-collision rate law agrees well with experimental removal data and provides a powerful design tool to assess the role of cleaning parameters, including process time, shear rate, dispensing flow rate, system geometry, solids concentration, and foam quality.
Cardiac Resynchronization Therapy: Do Women Benefit More Than Men? (2011)

Female CRT recipients seem to achieve greater survival benefit than male recipients. However, this benefit is majorly driven by nonischemic cardiomyopathy and other clinical factors.
Detection of circulating prostate carcinoma cells via an enhanced reverse transcriptase-polymerase chain reaction assay in patients with early stage prostate carcinoma (1997)

The detection of circulating prostate cells using RT-PCR occurs in approximately 25% of early stage prostate carcinoma patients and is independent of other established prognostic factors. In addition, a positive RT-PCR assay is a strong predictor of pathologic upstaging in patients with clinically organ-confined disease.
Supplementary Figure Legends from BET Bromodomain Inhibition Cooperates with PD-1 Blockade to Facilitate Antitumor Response in <i>Kras</i>-Mutant Non–Small Cell Lung Cancer (2023)

&lt;p&gt;figure legends for supplementary Table S1-S3 and supplementary Figure S1-S13&lt;/p&gt;
Deciphering the mechanisms underlying brain alterations and cognitive impairment in congenital myotonic dystrophy (2021)

Myotonic dystrophy type 1 (DM1) is a multisystemic and heterogeneous disorder caused by the expansion of CTG repeats in the 3' UTR of the myotonic dystrophy protein kinase (DMPK) gene. There is a congenital form (CDM1) of the disease characterized by severe hypotonia, respiratory insufficiency as well as developmental delays and intellectual disabilities. CDM1 infants manifest important brain structure abnormalities present from birth while, in contrast, older patients with adult-onset DM1 often present neurodegenerative features and milder progressive cognitive deficits. Promising therapies targeting central molecular mechanisms contributing to the symptoms of adult-onset DM1 are currently in development, but their relevance for treating cognitive impairment in CDM1, which seems to be a partially distinct neurodevelopmental disorder, remain to be elucidated. Here, we provide an update on the clinical presentation of CDM1 and review recent in vitro and in vivo models that have provided meaningful insights on its consequences in development, with a particular focus on the brain. We discuss how enhanced toxic gain-of-function of the mutated DMPK transcripts with larger CUG repeats and the resulting dysregulation of RNA-binding proteins may affect the developing cortex in utero. Because the methylation of CpG islets flanking the trinucleotide repeats has emerged as a strong biomarker of CDM1, we highlight the need to investigate the tissue-specific impacts of these chromatin modifications in the brain. Finally, we outline promising potential therapeutic treatments for CDM1 and propose future in vitro and in vivo models with great potential to shed light on this disease.
Genomic Landscapes of Pancreatic Neoplasia (2015)

Pancreatic cancer is a deadly disease with a dismal prognosis. However, recent advances in sequencing and bioinformatic technology have led to the systematic characterization of the genomes of all major tumor types in the pancreas. This characterization has revealed the unique genomic landscape of each tumor type. This knowledge will pave the way for improved diagnostic and therapeutic approaches to pancreatic tumors that take advantage of the genetic alterations in these neoplasms.