gebhart/patrepeval huggingface dataset:
A Systematic Review of Neoadjuvant Therapy Compared to the “Resection First” Approach for Patients with Borderline Resectable Pancreatic Adenocarcinoma (2014)

Background: Survival for patients with pancreatic adenocarcinoma continues to be poor. Patients with pancreatic adenocarcinoma that is deemed borderline resectable have imaging that shows disease involvement of the portal vein and/or superior mesenteric vein that is amenable to reconstruction or abutment (≤180 degrees) of the superior mesenteric artery. The best initial treatment for patients with borderline resectable pancreatic adenocarcinoma has yet to be determined. Proponents of neoadjuvant therapy purport its utility for patients with borderline resectable pancreatic adenocarcinoma with the intention of increasing the likelihood of a microscopically negative (R0) margin, but the consequences of this approach are not established. This study was undertaken to systematically review the outcomes for patients with borderline resectable pancreatic adenocarcinoma to compare neoadjuvant therapy to a “resection first” approach. Methods: A MEDLINE/PubMed search was undertaken to find all studies regarding patients who underwent neoadjuvant therapy for patients with borderline resectable pancreatic adenocarcinoma. Results: A total of 112 studies were found regarding borderline resectable pancreatic cancer. Fourteen studies contained cohorts of patients with borderline resectable pancreatic adenocarcinoma who received neoadjuvant therapy (n = 471 patients) or a resection-first approach (n = 76 patients). Resection after neoadjuvant therapy was undertaken for 233 (49%) patients. Neoadjuvant therapy followed by an R0 resection occurred for 42% of patients. For patients who underwent resection first, 71% (54/76) had an R0 margin. Conclusion: Patients with borderline resectable pancreatic adenocarcinoma were more often found to undergo neoadjuvant therapy than a “resection first” approach in the available literature. Although neoadjuvant therapy portends a high rate of R0 resections, less than half of the patients who undergo neoadjuvant therapy for borderline resectable pancreatic adenocarcinoma undergo resection. Patients who undergo “resection first” for borderline resectable pancreatic adenocarcinoma have an increased chance for a resection and an R0 margin compared to patients who undergo neoadjuvant therapy for borderline pancreatic adenocarcinoma.
Figure S4 from Mitochondrial Reprogramming Regulates Breast Cancer Progression (2023)

&lt;p&gt;SH3GL2 depletion in BCa cells.&lt;/p&gt;
Evaluation of Item-Based Top- N Recommendation Algorithms (2001)

The explosive growth of the world-wide-web and the emergence of e-commerce has led to the development of recommender systems---a personalized information filtering technology used to identify a set of N items that will be of interest to a certain user. User-based Collaborative filtering is the most successful technology for building recommender systems to date, and is extensively used in many commercial recommender systems. Unfortunately, the computational complexity of these methods grows linearly with the number of customers that in typical commercial applications can grow to be several millions. To address these scalability concerns item-based recommendation techniques have been developed that analyze the user-item matrix to identify relations between the different items, and use these relations to compute the list of recommendations.In this paper we present one such class of item-based recommendation algorithms that first determine the similarities between the various items and then used them to identify the set of items to be recommended. The key steps in this class of algorithms are (i) the method used to compute the similarity between the items, and (ii) the method used to combine these similarities in order to compute the similarity between a basket of items and a candidate recommender item. Our experimental evaluation on five different datasets show that the proposed item-based algorithms are up to 28 times faster than the traditional user-neighborhood based recommender systems and provide recommendations whose quality is up to 27% better.
Electromagnetic Scattering From Multiple Single-Walled Carbon Nanotubes Having Tumbleweed Configurations (2017)

Carbon nanotubes (CNTs) exhibit highly complicated structures when incorporated in composites and are neither perfectly straight nor aligned in any one direction. Recently, the “clumpy” structure of multiple aggregated CNTs has been likened to desert tumbleweeds. The goal of this paper is to quantify the electromagnetic scattering characteristics of CNTs in the tumbleweed configuration using classical electromagnetic simulations. The simulation results show that the first-plasmon resonance, exhibited by an individual CNT, splits into multiple resonances when multiple CNTs agglomerate into tumbleweed configurations. The number of the resonances increases linearly with the number of CNTs inside the tumbleweed. The second-plasmon resonance exhibits similar splitting behavior. This splitting in the plasmon resonances is caused by the asymmetry of shapes of CNTs and their proximity to each other. If sufficient CNTs agglomerate, the split first-plasmon and second-plasmon resonances overlap, leading to an overall broadband behavior. These results indicate the importance of precise modeling of CNT shapes and the distribution of shapes on the electromagnetic response. Our computations qualitatively explain the broadband response of CNT films and composites and should aid in the development of novel broadband materials and devices based on CNTs.
Insulin Induces Phosphorylation of Serine Residues of Translationally Controlled Tumor Protein in 293T Cells (2015)

Insulin induces the activation of Na,K-ATPase while translationally controlled tumor protein (TCTP) inhibits this enzyme and the associated pump activity. Because binding of insulin with its membrane receptor is known to mediate the phosphorylation of multiple intracellular proteins, phosphorylation of TCTP by insulin might be related to the sodium pump regulation. We therefore examined whether insulin induces TCTP phosphorylation in embryonic kidney 293T cells. Using immunoprecipitation and Western blotting, we found that insulin phosphorylates serine (Ser) residues of TCTP. Following fractionation of the insulin-treated cells into cytosol and membrane fractions, phosphorylated TCTP at its Ser residue (p-Ser-TCTP) was detected exclusively in the cytosolic part and not in the membrane fraction. Phosphorylation of TCTP reached maximum in about 10 min after insulin treatment in 293T cells. In studies of cell-type specificity of insulin-mediated phosphorylation of TCTP, insulin did not phosphorylate TCTP in HeLa cells. Computational prediction and immunoprecipitation using several constructs having Ser to Ala mutation at potential p-Ser sites of TCTP revealed that insulin phosphorylated the serine-9 and -15 residues of TCTP. Elucidations of how insulin-mediated TCTP phosphorylation promotes Na,K-ATPase activation, may offer potential therapeutic approaches to diseases associated with vascular activity and sodium pump dysregulation.
A Novel Blaschke Unwinding Adaptive-Fourier-Decomposition-Based Signal Compression Algorithm With Application on ECG Signals (2018)

This paper presents a novel signal compression algorithm based on the Blaschke unwinding adaptive Fourier decomposition (AFD). The Blaschke unwinding AFD is a newly developed signal decomposition theory. It utilizes the Nevanlinna factorization and the maximal selection principle in each decomposition step, and achieves a faster convergence rate with higher fidelity. The proposed compression algorithm is applied to the electrocardiogram signal. To assess the performance of the proposed compression algorithm, in addition to the generic assessment criteria, we consider the less discussed criteria related to the clinical needs-for the heart rate variability analysis purpose, how accurate the R-peak information is preserved is evaluated. The experiments are conducted on the MIT-BIH arrhythmia benchmark database. The results show that the proposed algorithm performs better than other state-of-the-art approaches. Meanwhile, it also well preserves the R-peak information.
CAMK2-Dependent Signaling in Neurons Is Essential for Survival (2019)

Ca<sup>2+</sup>/calmodulin-dependent protein kinase II (CAMK2) is a key player in synaptic plasticity and memory formation. Mutations in <i>Camk2a</i> or <i>Camk2b</i> cause intellectual disability in humans, and severe plasticity and learning deficits in mice, indicating unique functions for each isoform. However, considering the high homology between CAMK2A and CAMK2B, it is conceivable that for critical functions, one isoform compensates for the absence of the other, and that the full functional spectrum of neuronal CAMK2 remains to be revealed.Here we show that germline as well as adult deletion of both CAMK2 isoforms in male or female mice is lethal. Moreover, Ca<sup>2+</sup>-dependent activity as well as autonomous activity of CAMK2 is essential for survival. Loss of both CAMK2 isoforms abolished LTP, whereas synaptic transmission remained intact. The double-mutants showed no gross morphological changes of the brain, and in contrast to the long-considered role for CAMK2 in the structural organization of the postsynaptic density (PSD), deletion of both CAMK2 isoforms did not affect the biochemical composition of the PSD. Together, these results reveal an essential role for CAMK2 signaling in early postnatal development as well as the mature brain, and indicate that the full spectrum of CAMK2 requirements cannot be revealed in the single mutants because of partial overlapping functions of CAMK2A and CAMK2B.<b>SIGNIFICANCE STATEMENT</b> CAMK2A and CAMK2B have been studied for over 30 years for their role in neuronal functioning. However, most studies were performed using single knock-out mice. Because the two isoforms show high homology with respect to structure and function, it is likely that some redundancy exists between the two isoforms, meaning that for critical functions CAMK2B compensates for the absence of CAMK2A and vice versa, leaving these functions to uncover. In this study, we generated <i>Camk2a/Camk2b</i> double-mutant mice, and observed that loss of CAMK2, as well as the loss of Ca<sup>2+</sup>-dependent and Ca<sup>2+</sup>-independent activity of CAMK2 is lethal. These results indicate that despite 30 years of research the full spectrum of CAMK2 functioning in neurons remains to be unraveled.
Assessment of P- to delta-wave interval and its relationship with accessory pathway properties in patients with pre-excitation (2021)

Our results demonstrate that there was a strong correlation between the P- to delta-wave interval and universally accepted risk factors, such as low age, low APERP and atrial fibrillation inducibility. Further studies with larger patient groups and follow-up data are needed to appraise its predictive value.
Calmodulin‐like calcium‐binding protein identified in calcium‐rich mineral deposits from freshwater mussel gills (1988)

Abstract Extracellular calcium concretions found in the gills of freshwater unionids are largely inorganic, containing calcium and phosphate. The organic fraction of the isolated concretions accounts for 25% of their dry weight as determined by ashing. The organic fraction of isolated concretions was examined using SDS‐polyacrylamide electrophoresis. The concretion fraction is separated into 13–14 protein bands. These bands can be further differentiated into EDTA soluble proteins and insoluble core proteins. One of the soluble proteins has a molecular weight of approximately 17,000 daltons (Da) and comigrates with authentic vertebrate calmodulin. The 17,000‐Da concretion protein cross‐reacts with sheep IgG prepared against bovine brain calmodulin as shown by immunoblot. Rabbits and mice, challenged with the entire concretion organic fraction, produce an IgG fraction which always recognizes an epitope of the 17,000‐Da protein as the major antigenic determinant. This same protein is also a calcium binding protein as shown by 45 Ca autoradiography even after heat and SDS/mercaptoethanol treatment. To determine that this protein was not bound to the concretions as an artifact of the isolation procedures, immunocytochemical procedures were used to localize the antigenicity to 17,000‐Da and vertebrate calmodulin in situ. Immunocytochemical localization indicates the protein is present on the concretions in situ but documents that the majority of this protein is located in concretion‐forming cells. Electron microscopic immunocytochemistry demonstrates that the protein is found largely in early concretion‐forming cells in protein granules formed before concretion architecture is observed. This may imply that the protein is likely important in the initiation of concretion formation, and is only a residual protein as found on the extracellular concretions.
PD-1/PD-L1 pathway: an adaptive immune resistance mechanism to immunogenic chemotherapy in colorectal cancer (2018)

Chemotherapy is currently evaluated in order to enhance the efficacy of immune checkpoint blockade (ICB) therapy in colorectal cancer. However, the mechanisms by which these drugs could synergize with ICB remains unclear. The impact of chemotherapy on the PD-1/PD-L1 pathway and the resulting anticancer immune responses was assessed in two mouse models of colorectal cancer and validated in tumor samples from metastatic colorectal cancer patients that received neoadjuvant treatment. We demonstrated that 5-Fluorouracil plus Oxaliplatin (Folfox) drove complete tumor cure in mice when combined to anti-PD-1 treatment, while each monotherapy failed. This synergistic effect relies on the ability of Folfox to induce tumor infiltration by activated PD-1<sup>+</sup> CD8 T cells in a T-bet dependent manner. This effect was concomitantly associated to the expression of PD-L1 on tumor cells driven by IFN-γ secreted by PD-1+ CD8 T cells, indicating that Folfox triggers tumor adaptive immune resistance. Finally, we observed an induction of PD-L1 expression and high CD8 T cell infiltration in the tumor microenvironment of colorectal cancer patients treated by Folfox regimen. Our study delineates a molecular pathway involved in Folfox-induced adaptive immune resistance in colorectal cancer. The results strongly support the use of immune checkpoint blockade therapy in combination with chemotherapies like Folfox.
Supplementary Table S2 from Safety and Tolerability of Bintrafusp Alfa, a Bifunctional Fusion Protein Targeting TGFβ and PD-L1, in Asian Patients with Pretreated Recurrent or Refractory Gastric Cancer (2023)

&lt;p&gt;Supplementary Table S2 shows the study inclusion and exclusion criteria.&lt;/p&gt;
Research Note: Effect of Dietary Phosphorus Levels on Performance of Turkey Breeder Hens (1989)

One hundred 30-wk-old medium weight white Orlopp turkey breeder hens were equally divided into four treatment groups according to the level of available P in the diet (.15, .30, .50, and .70%, respectively). The P provided in the basal diet (.15% available, .35% total) was from cereal grains and soybean meal. No supplemental phosphate was added. During the 20-wk experiment, there were no differences in number of days required to come into lay and in subsequent egg production. Specific gravity, egg weight, number of shell pores, and body weight were similar under all treatments. The P levels of birds fed the four diets were 4.82, 4.93, 4.93, and 4.94 mg/100 mL, respectively, in serum and in femur were 15.8, 16.1, 16.8, and 16.4%, respectively. The P levels were slightly lower in birds fed the diet without added P. Excreta P levels (1.93, 2.49, 2.81, and 3.10%, respectively, in birds fed the four diets) were significantly (P less than .05) higher with each successive increase in dietary P. Hens fed diets containing .50 or .70% available P retained (46.9 and 54.8%, respectively) significantly more P than those fed diets containing .15 or .30% available P (28.1 and 33.8%, respectively). Fertility (76, 93, 90, and 89%, respectively) was significantly lower (P less than .05) from feeding the diet without added P. Hatchability rates of fertile eggs were similar for all treatments.
Glucose metabolism, gray matter structure, and memory decline in subjective memory impairment (2012)

The cross-sectional difference in 2 independent neuroimaging modalities indicates early AD pathology in SMI. The poorer memory performance at follow-up and the association of reduced longitudinal memory performance with hypometabolism in the precuneus at baseline support the concept of SMI as the earliest manifestation of AD.
On-the-fly detection of novel objects in indoor environments (2017)

Many robotic applications require the detection of new objects in known environments. Common approaches navigate in the environment using pre-defined waypoints and segment the scene at these waypoints. Without knowing where to find new objects, this process can be time-consuming and prone to detecting false positives. To overcome these limitations we propose an approach that combines navigation and attention in order to detect novel objects rapidly. We exploit the octomap, created by the robot while it navigates in the environment, as a pre-attention filter to suggest potential regions of interest. These regions are then visited to obtain a close-up view for better object detection and recognition. We evaluate our approach in a simulated as well as a real environment. The experiments show that our approach outperforms previous approaches in terms of runtime and the number of segmentation actions required to find all novel objects in the environment.
Core-Shell Fine Structure and Size-Dependent Morphology of Dealloyed Pt Bimetallic Nanoparticle Fuel Cell Electrocatalysts (2013)

Electrochemical dealloying is a simple facile synthetic approach to prepare advanced core-shell nanocatalysts with improved activity for the oxygen reduction reaction (ORR). The catalytically active core-shell structure forms by selective dissolution of the less noble metal from a uniform Pt-poor alloy precursor nanoparticle. However, the processes during the dealloying of nanoscale alloys are still unclear. We present a comparative structural and elemental sensitive investigation of dealloyed Pt-M (M=Ni,Cu,Co) alloy nanoparticles in their catalytically most active state. Based on the Cs-corrected high resolution scanning transmission electron microscopy (HR-STEM) results, we have uncovered a number of different dominant morphological structure types for Pt alloys as a function of their particle size. With increasing particle size the dealloyed particles show increased complex self-organized structures such as multiple cores with irregular shape and nanopores. The size-composition-structure relations link the dealloyed nanoparticles with dealloyed bulk materials to minimize the existing material gap.
New approach to endotoxic and septic shock by means of polymyxin B immobilized fiber. (1989)

Endotoxin shock therapy has not been successfully dealt with pharmacologically. Circulation of endotoxins in the blood is an important factor in the pathogenesis and clinical symptoms of endotoxic shock. We have recently developed polymyxin immobilized fiber (PMX-F) as a biomaterial for selectively detoxifying endotoxins. In ex vivo experiments, direct hemoperfusion (DHP) by PMX-F was performed on dogs injected with purified endotoxin. Only one of eight survived in the control group, but ten of 12 survived in the group receiving DHP with PMX-F. Mortality in the treated group decreased remarkably. Thus, the results indicate the efficacy of PMX-F in neutralizing endotoxins. By the same method as already mentioned, DHP with PMX-F was carried out on live dogs with Escherichia coli induced sepsis. All of the dogs in the control group died within 18 hours after bacterial infusion. All of the dogs in the treated group, however, survived for more than three days. Two of the five dogs are still alive. One of the remaining two survived for seven days and the other, 14. We found that PMX-F treatment prolonged or increased the survival rate in the endotoxic and septic dogs.
Base-Catalyzed Depolymerization of Lignin with Heterogeneous Catalysts: Cooperative Research and Development Final Report, CRADA Number CRD-13-513 (2015)

We will synthesize and screen solid catalysts for the depolymerization of lignin to monomeric and oligomeric oxygenated species, which could be fractionated and integrated into refinery intermediate streams for selective upgrading, or catalytically upgraded to fuels and chemicals. This work will primarily focus on the synthesis and application of layered double hydroxides (LDHs) as recyclable, heterogeneous catalysts for depolymerization of lignin model compounds and softwood lignin. LDHs have been shown in our group to offer good supports and catalysts to promote base-catalyzed depolymerization of lignin model compounds and in preliminary experiments for the depolymerization of lignin from an Organosolv process. We will also include additional catalyst supports such as silica, alumina, and carbon as identified in ongoing and past efforts at NREL. This work will consist of two tasks. Overall, this work will be synergistic with ongoing efforts at NREL, funded by the DOE Biomass Program, on the development of catalysts for lignin depolymerization in the context of biochemical and thermochemical conversion of corn stover and other biomass feedstocks to advanced fuels and chemicals.
Neuropathologic Substrate of Mild Cognitive Impairment (2006)

In patients with amnestic MCI who were followed longitudinally, the early changes of Alzheimer disease were present. The NFTs were slightly more prominent than beta-amyloid peptide deposition in the progression from normal to MCI to EAD. Ventromedial temporal lobe NFTs probably represent the substrate for memory decline in MCI. From a neuropathologic perspective, it appears that amnestic MCI is, in reality, EAD.
Hydrolases of the ILR1-like family of Arabidopsis thaliana modulate auxin response by regulating auxin homeostasis in the endoplasmic reticulum (2016)

Amide-linked conjugates of indole-3-acetic acid (IAA) have been identified in most plant species. They function in storage, inactivation or inhibition of the growth regulator auxin. We investigated how the major known endogenous amide-linked IAA conjugates with auxin-like activity act in auxin signaling and what role ILR1-like proteins play in this process in Arabidopsis. We used a genetically encoded auxin sensor to show that IAA-Leu, IAA-Ala and IAA-Phe act through the TIR1-dependent signaling pathway. Furthermore, by using the sensor as a free IAA reporter, we followed conjugate hydrolysis mediated by ILR1, ILL2 and IAR3 in plant cells and correlated the activity of the hydrolases with a modulation of auxin response. The conjugate preferences that we observed are in agreement with available in vitro data for ILR1. Moreover, we identified IAA-Leu as an additional substrate for IAR3 and showed that ILL2 has a more moderate kinetic performance than observed in vitro. Finally, we proved that IAR3, ILL2 and ILR1 reside in the endoplasmic reticulum, indicating that in this compartment the hydrolases regulate the rates of amido-IAA hydrolysis which results in activation of auxin signaling.