gebhart/patrepeval huggingface dataset:
Highly potent soluble amyloid-β seeds in human Alzheimer brain but not cerebrospinal fluid (2014)

The soluble fraction of brain samples from patients with Alzheimer's disease contains highly biologically active amyloid-β seeds. In this study, we sought to assess the potency of soluble amyloid-β seeds derived from the brain and cerebrospinal fluid. Soluble Alzheimer's disease brain extracts were serially diluted and then injected into the hippocampus of young, APP transgenic mice. Eight months later, seeded amyloid-β deposition was evident even when the hippocampus received subattomole amounts of brain-derived amyloid-β. In contrast, cerebrospinal fluid from patients with Alzheimer's disease, which contained more than 10-fold higher levels of amyloid-β peptide than the most concentrated soluble brain extracts, did not induce detectable seeding activity in vivo. Similarly, cerebrospinal fluid from aged APP-transgenic donor mice failed to induce cerebral amyloid-β deposition. In comparison to the soluble brain fraction, cerebrospinal fluid largely lacked N-terminally truncated amyloid-β species and exhibited smaller amyloid-β-positive particles, features that may contribute to the lack of in vivo seeding by cerebrospinal fluid. Interestingly, the same cerebrospinal fluid showed at least some seeding activity in an in vitro assay. The present results indicate that the biological seeding activity of soluble amyloid-β species is orders of magnitude greater in brain extracts than in the cerebrospinal fluid.
Data from A Bispecific Antibody Antagonizes Prosurvival CD40 Signaling and Promotes Vγ9Vδ2 T cell–Mediated Antitumor Responses in Human B-cell Malignancies (2023)

&lt;div&gt;Abstract&lt;p&gt;Novel T cell–based therapies for the treatment of B-cell malignancies, such as chronic lymphocytic leukemia (CLL) and multiple myeloma (MM), are thought to have strong potential. Progress, however, has been hampered by low efficacy and high toxicity. Tumor targeting by Vγ9Vδ2 T cells, a conserved T-cell subset with potent intrinsic antitumor properties, mediated by a bispecific antibody represents a novel approach promising high efficacy with limited toxicity. Here, we describe the generation of a bispecific Vγ9Vδ2 T-cell engager directed against CD40, which, due to its overexpression and biological footprint in malignant B cells, represents an attractive target. The CD40-targeting moiety of the bispecific antibody was selected because it can prevent CD40L-induced prosurvival signaling and reduce CD40-mediated resistance of CLL cells to venetoclax. Selective activation of Vγ9Vδ2 T cells in the presence of CD40&lt;sup&gt;+&lt;/sup&gt; tumor cells induced potent Vγ9Vδ2 T-cell degranulation, cytotoxicity against CLL and MM cells &lt;i&gt;in vitro&lt;/i&gt;, and &lt;i&gt;in vivo&lt;/i&gt; control of MM in a xenograft model. The CD40-bispecific γδ T-cell engager demonstrated lysis of leukemic cells by autologous Vγ9Vδ2 T cells present in patient-derived samples. Taken together, our CD40 bispecific γδ T-cell engager increased the sensitivity of leukemic cells to apoptosis and induced a potent Vγ9Vδ2 T cell–dependent antileukemic response. It may, therefore, represent a potential candidate for the development of novel treatments for B-cell malignancies.&lt;/p&gt;&lt;/div&gt;
The Taphonomy of a Sacrifice: Burial 6 of the Patio Hundido at el Teul (2012)

El Teul’s eighteen centuries of continuous occupation, from ca. 200 b. c. e. till the Spanish conquest in 1531 offers a unique opportunity to understand aspects of ancient society in Southern Zacatecas. This poster focuses on a ritually-sacrificed male whose body was deposited as an offering in one of the main architectural complexes of the site during the early to mid-Classic (ca. 200 d.C. – 400/450 d.C.). Ritual landscape models currently applied to larger sites such as Teotihuacán using Huichol cosmology suggest the possible correspondence of this building with ritual sacrifice related to winter solstice with Venus playing an active role.
Enhanced levels of hyaluronan in lungs of patients with COPD: relationship with lung function and local inflammation (2005)

These data indicate a relationship between HA levels, local inflammation and severity of disease, and suggest enhanced breakdown of HA in the lungs of patients with COPD.
Variations in 1-octen-3-ol and lipoxygenase gene expression in the oyster mushroom Pleurotus ostreatus according to fruiting body development, tissue specificity, maturity, and postharvest storage (2019)

1-Octen-3-ol is considered a major contributor to the characteristic mushroom aroma. It has been proposed that in the oyster mushroom Pleurotus ostreatus, 1-octen-3-ol is synthesized through two pathways comprising either 13-hydroperoxy-9Z,11E-octadecadienoic acid (13-HPOD) or 10-hydroperoxy-8E,12Z-octadecadienoic acid as an intermediate, and that 13-HPOD is produced by the oxidation of linoleic acid by lipoxygenase (LOX). However, information on 1-octen-3-ol in this mushroom remains limited. This study investigated variations in 1-octen-3-ol and the LOX gene (Polox1 and Polox2) expression together with LOX activity in P. ostreatus, according to fruiting body development, tissue specificity, maturity, and postharvest storage. 1-Octen-3-ol content was abundant in the stipe of medium-sized fruiting bodies (40–50 mm cap diam), but decreased after 2 d of storage at 4 °C. During fruiting body development, changes in LOX activity mimicked changes in transcript levels of Polox1, which was much more abundantly expressed than Polox2. The changes in LOX activity were different from changes in 1-octen-3-ol levels according to fruiting body development, maturity, and postharvest storage. Our investigation suggests that medium-sized fruiting bodies that were not subjected to long-term storage would have a good aroma quality and that there is no correlation between 1-octen-3-ol synthesis and LOX activity, which is largely dependent on Polox1 expression.
Protocol: a rapid and economical procedure for purification of plasmid or plant DNA with diverse applications in plant biology (2010)

Research in plant molecular biology involves DNA purification on a daily basis. Although different commercial kits enable convenient extraction of high-quality DNA from E. coli cells, PCR and agarose gel samples as well as plant tissues, each kit is designed for a particular type of DNA extraction work, and the cost of purchasing these kits over a long run can be considerable. Furthermore, a simple method for the isolation of binary plasmid from Agrobacterium tumefaciens cells with satisfactory yield is lacking. Here we describe an easy protocol using homemade silicon dioxide matrix and seven simple solutions for DNA extraction from E. coli and A. tumefaciens cells, PCR and restriction digests, agarose gel slices, and plant tissues. Compared with the commercial kits, this protocol allows rapid DNA purification from diverse sources with comparable yield and purity at negligible cost. Following this protocol, we have demonstrated: (1) DNA fragments as small as a MYC-epitope tag coding sequence can be successfully recovered from an agarose gel slice; (2) Miniprep DNA from E. coli can be eluted with as little as 5 mul water, leading to high DNA concentrations (>1 mug/mul) for efficient biolistic bombardment of Arabidopsis seedlings, polyethylene glycol (PEG)-mediated Arabidopsis protoplast transfection and maize protoplast electroporation; (3) Binary plasmid DNA prepared from A. tumefaciens is suitable for verification by restriction analysis without the need for large scale propagation; (4) High-quality genomic DNA is readily isolated from several plant species including Arabidopsis, tobacco and maize. Thus, the silicon dioxide matrix-based DNA purification protocol offers an easy, efficient and economical way to extract DNA for various purposes in plant research.
Equivalence between Two Results Providing Polyhedral Contractive Sets for Discrete-Time Linear Systems with Arbitrary Switching (2019)

The paper belongs to the area of qualitative analysis of the dynamics for discrete-time arbitrary switching linear systems. The purpose of our research is to develop a rigorous comparative study between two criteria for testing the existence of λ-contractive polyhedral sets with respect to the switching systems. Despite the common objective of the two criteria, their connections at the level of the mathematical backgrounds have been insufficiently explored. These backgrounds are relatively distanced, namely the operation with convex sets versus solvability of several matrix equalities, with inequality constraints. Our work proposes complete mathematical results with accompanying proofs, which are able to explain all the links that are currently missing from the literature. These theoretical results are illustrated by a numerical example run in Matlab, which also offers visual support for the construction and utilization of λ-contractive polyhedral sets.
Tinosporaside from Tinospora cordifolia Encourages Skeletal Muscle Glucose Transport through Both PI-3-Kinase- and AMPK-Dependent Mechanisms (2023)

The stem of <i>Tinospora cordifolia</i> has been traditionally used in traditional Indian systems of medicine for blood sugar control, without the knowledge of the underlying mechanism and chemical constitution responsible for the observed anti-diabetic effect. In the present study, Tinosporaside, a diterpenoid isolated from the stem of <i>T. cordifolia</i>, was investigated for its effects on glucose utilization in skeletal muscle cells, which was followed by determining the anti-hyperglycemic efficacy in our diabetic db/db mice model. We found that tinosporaside augmented glucose uptake by increasing the translocation of GLUT4 to the plasma membrane in L6 myotubes, upon prolonged exposure for 16 h. Moreover, tinosporaside treatment significantly increased the phosphorylation of protein kinase B/AKT (Ser-473) and 5' AMP-activated protein kinase (AMPK, Thr-172). These effects were abolished in the presence of the wortmannin and compound C. Administration of tinosporaside to db/db mice improved glucose tolerance and peripheral insulin sensitivity associated with increased gene expression and phosphorylation of the markers of phosphoinositide 3-kinases (PI3Ks) and AMPK signaling in skeletal muscle tissue. The findings revealed that tinosporaside exerted its antidiabetic efficacy by enhancing the rate of glucose utilization in skeletal muscle, mediated by PI3K- and AMPK-dependent signaling mechanisms.
Brain phenotyping in Moebius syndrome and other congenital facial weakness disorders by diffusion MRI morphometry (2020)

In this study, we used a novel imaging technique, DTI (diffusion tensor imaging)-driven tensor-based morphometry, to investigate brain anatomy in subjects diagnosed with Moebius syndrome (<i>n</i> = 21), other congenital facial weakness disorders (<i>n</i> = 9) and healthy controls (<i>n</i> = 15). First, we selected a subgroup of subjects who satisfied the minimum diagnostic criteria for Moebius syndrome with only mild additional neurological findings. Compared to controls, in this cohort, we found a small region of highly significant volumetric reduction in the paramedian pontine reticular formation and the medial longitudinal fasciculus, important structures for the initiation and coordination of conjugate horizontal gaze. Subsequently, we tested if volume measurements from this region could help differentiate individual subjects of the different cohorts that were included in our study. We found that this region allowed discriminating Moebius syndrome subjects from congenital facial weakness disorders and healthy controls with high sensitivity (94%) and specificity (89%). Interestingly, this region was normal in congenital facial weakness subjects with oculomotor deficits of myopathic origin, who would have been classified as Moebius on the basis of purely clinical diagnostic criteria, indicating a potential role for diffusion MRI morphometry for differential diagnosis in this condition. When the entire Moebius syndrome cohort was compared to healthy controls, in addition to this 'landmark' region, other areas of significantly reduced volume in the brainstem emerged, including the location of the nuclei and fibres of cranial nerve VI (abducens nerve), and fibres of cranial nerve VII (facial nerve), and a more rostral portion of the medial longitudinal fasciculus. The high sensitivity and specificity of DTI-driven tensor-based morphometry in reliably detecting very small areas of volumetric abnormality found in this study suggest broader applications of this analysis in personalized medicine to detect hypoplasia or atrophy of small pathways and/or brainstem nuclei in other neurological disorders.
5D Data Storage by Ultrafast Laser Nanostructuring in Glass (2013)

The high-density five dimensional data storage with ultrafast laser writing is demonstrated. The text file is recorded by polarization controlled self-assembled form birefringence and retrieved in glass opening the era of unlimited lifetime data storage.
Macrophage sensing of single-walled carbon nanotubes via Toll-like receptors (2018)

Carbon-based nanomaterials including carbon nanotubes (CNTs) have been shown to trigger inflammation. However, how these materials are 'sensed' by immune cells is not known. Here we compared the effects of two carbon-based nanomaterials, single-walled CNTs (SWCNTs) and graphene oxide (GO), on primary human monocyte-derived macrophages. Genome-wide transcriptomics assessment was performed at sub-cytotoxic doses. Pathway analysis of the microarray data revealed pronounced effects on chemokine-encoding genes in macrophages exposed to SWCNTs, but not in response to GO, and these results were validated by multiplex array-based cytokine and chemokine profiling. Conditioned medium from SWCNT-exposed cells acted as a chemoattractant for dendritic cells. Chemokine secretion was reduced upon inhibition of NF-κB, as predicted by upstream regulator analysis of the transcriptomics data, and Toll-like receptors (TLRs) and their adaptor molecule, MyD88 were shown to be important for CCL5 secretion. Moreover, a specific role for TLR2/4 was confirmed by using reporter cell lines. Computational studies to elucidate how SWCNTs may interact with TLR4 in the absence of a protein corona suggested that binding is guided mainly by hydrophobic interactions. Taken together, these results imply that CNTs may be 'sensed' as pathogens by immune cells.
Pancreas transplantation in nonuremic, type I diabetic recipients. (1988)

Between July 1978 and January 1988, 111 of 210 pancreas transplants were in nonuremic, nonkidney (NUNK) recipients in whom complications of diabetes were judged more serious than the potential side effects of antirejection therapy. In all NUNK cases, the 1-year patient survival rate (PSR) and graft survival rate (GSR) were 90% and 39%. Since November 1984, 1-year PSR and GSR for 62 NUNK recipients of pancreas transplants alone (PTA) were 93% and 48%, compared to 89% and 37% for 28 pancreas transplants after (PAK) and 89% and 73% for 20 simultaneous (SPK) with a kidney transplant. The 1-year GSR for 1984-88 technically successful (TS) PTA cases (n = 47) was 63%, versus 75% for PAK (n = 13) and 86% for SPK (n = 17) cases. The 1-year GSRs, by technique and source for 1984-88 PTA cases, were 58% for bladder-drained cadaver (n = 30), 51% for enteric-drained related (n = 32), and 29% for enteric-drained cadaver (n = 17) donor transplants, and 75% (n = 24), 77% (n = 16), and 38% (n = 13) for the corresponding TS cases. Of NUNK recipients, 35 have had grafts function for more than 1 year and all but 3 were treated with cyclosporine (CsA). In the CsA-treated recipients, serum creatinine increased and creatinine clearances decreased by a magnitude of 40% during the first 6 months but thereafter remained stable in all but 2 patients. In the patients with functioning grafts studied at 1 year, retinopathy remained stable in 59% and progressed in 41% of the eyes (n = 39). Motor nerve conduction velocities were significantly increased and muscle action potentials remained stable in 24 patients with functioning grafts studied at 1 year, while in 14 patients in whom transplants failed there was a significant decrease in evoked muscle action potentials. A sustained euglycemic, insulin-independent state can be established in nonuremic, nonkidney diabetic recipients of pancreas transplants alone, with a beneficial effect on neuropathy, lack of an immediate benefit on advanced retinopathy, and an effect on nephropathy compounded by the influence of CsA on renal function.
Manganese Oxide as a Promoter for Copper Catalysts in CO2 and CO Hydrogenation (2022)

In this work, we discuss the role of manganese oxide as a promoter in Cu catalysts supported on graphitic carbon during hydrogenation of CO<sub>2</sub> and CO. MnO<sub>x</sub> is a selectivity modifier in an H<sub>2</sub>/CO<sub>2</sub> feed and is a highly effective activity promoter in an H<sub>2</sub>/CO feed. Interestingly, the presence of MnO<sub>x</sub> suppresses the methanol formation from CO<sub>2</sub> (TOF of 0.7 ⋅ 10<sup>-3</sup> s<sup>-1</sup> at 533 K and 40 bar) and enhances the low-temperature reverse water-gas shift reaction (TOF of 5.7 ⋅ 10<sup>-3</sup> s<sup>-1</sup>) with a selectivity to CO of 87 %<sub>C</sub>. Using time-resolved XAS at high temperatures and pressures, we find significant absorption of CO<sub>2</sub> to the MnO, which is reversed if CO<sub>2</sub> is removed from the feed. This work reveals fundamental differences in the promoting effect of MnO<sub>x</sub> and ZnO<sub>x</sub> and contributes to a better understanding of the role of reducible oxide promoters in Cu-based hydrogenation catalysts.
Single Center Real-World Experience of Daratumumab and Extra-Medullary Myeloma (2018)

Abstract Background: Daratumumab (Dara) was recently FDA approved for the treatment of relapsed/refractory multiple myeloma (RRMM). We evaluated a real-world single-center experience of Dara salvage therapy for RRMM. Methods: Patients treated at the University of Florida with Dara for RRMM between January 2016 and February 2018 were included. Data was collected by chart review and analyzed for patient demographics, disease characteristics, treatment, and outcomes. Results: 25 patients (13 as monotherapy and 12 in combination) were included, with a median age of 63 (range, 42-86) years. Median time from MM diagnosis to Dara initiation was 51.3 (range, 8.4 -162.3) months. The median duration of Dara therapy was 72 days (range, 7 - 622). The median number of Dara doses was 7 (range, 2- 49). The best response to DARA was Very Good Partial Response (VGPR) in 1 (4%), Partial Response (PR) in 17 (68%), while 7 (28%) had Progressive Disease (PD). Overall Response Rate (ORR) to Dara was 72%. By the end of the study period, another 11 (44%) patients progressed while on DARA with a total of 18 (72%) patients having PD at the time of analysis. Estimated median progression free survival (PFS) after starting Dara was 155 days (95% CI: 21 - 289) and estimated median overall survival (OS) in the entire cohort was 11.7 months (95% CI: 4.2 - 19.2). Post DARA, 1 (4%) patient with VGPR underwent ASCT, while 9 (36%) went on to have other therapies which included HyperCVAD, Melphalan, and clinical trials, and 8 (32%) were treated with only best supportive care. Of 18 patients who had PD, 10 (40%) patients had a progressive extramedullary disease (EMD), of whom 6 (24%) had EMD prior to starting Dara, while another 4 (16%) patients developed new EMD while on Dara. PFS in the EMD cohort was 63 days (95% CI: 23 - 103), which was shorter than patients with no EMD (333 days; 95% CI: 42 - 624) (P= 0.08). Estimated median OS in patients with EMD was 5.4 months while in patients with no EMD was 16.1 months (p =0.16). Conclusions: DARA therapy does have good ORR (72%) in RRMM, however, there was an unusually high incidence of progressive or newly diagnosed EMD in RRMM patients treated with Dara/Dara-containing regimens, suggesting that Dara may not be effective in treating or preventing EMD. Moreover, we noticed patients who have EMD or develop new EMD tends to have worse outcomes. The underlying escape mechanism for EMD remains unknown and warrants further investigation. Table. Table. Disclosures No relevant conflicts of interest to declare.
Pinpointing Hidden IoT Devices via Spatial-temporal Traffic Fingerprinting (2020)

With the popularization of Internet of Things (IoT) devices in smart home and industry fields, a huge number of IoT devices are connected to the Internet. However, what devices are connected to a network may not be known by the Internet Service Provider (ISP), since many IoT devices are placed within small networks (e.g., home networks) and are hidden behind network address translation (NAT). Without pinpointing IoT devices in a network, it is unlikely for the ISP to appropriately configure security policies and effectively manage the network. In this paper, we design an efficient and scalable system via spatial-temporal traffic fingerprinting. Our system can accurately identify typical IoT devices in a network, with the additional capability of identifying what devices are hidden behind NAT and how many they are. Through extensive evaluation, we demonstrate that the system can generally identify IoT devices with an F-Score above 0.999, and estimate the number of the same type of IoT device behind NAT with an average error below 5%. We also perform small-scale (labor-intensive) experiments to show that our system is promising in detecting user-IoT interactions.
Production of Steryl Esters Using Alternative Sources of Sterols and Free Fatty Acids: Modeling and Guidelines (2014)

Enzymatic esterification reactions for the production of steryl esters were conducted using different sources of sterols and free fatty acids from mixtures of vegetable oil deodorizer distillates and refined oil. This work discusses the possibility of using free fatty acids from alternative and less expensive sources, determining their influence on the yield of steryl ester production as well as on the validity of a kinetic model previously developed for defined reaction medium composition. The extrapolation capacity of such a model was investigated, identifying the cases where a lack of model fitting was observed and establishing the range of conditions for model applicability. Based on a sensitivity analysis, guidelines to obtain acceptable yields (>80%) were established. This paper shows that the use of alternative sources of sterols and free fatty acids for the production of steryl esters is possible; however, there are constraints and guidelines that have to be taken into account.
Lipid growth requirement and influence of lipid supplement on fatty acid and aldehyde composition of Syntrophococcus sucromutans (1989)

Results concerning the ruminal fluid growth requirement of the ruminal acetogen, Syntrophococcus sucromutans, indicate that octadecenoic acid isomers satisfy this essential requirement. Complex lipids, such as triglycerides and phospholipids, can also support growth. The cellular fatty acid and aldehyde composition closely reflects that of the lipid supplement provided to the cells. Up to 98% of the fatty acids and 80% of the fatty aldehydes are identical in chain length and degree of unsaturation to the octadecenoic acid supplement provided in the medium. S. sucromutans shows a tendency to have a greater proportion of the aldehyde form among its 18 carbon chains than it does with the shorter-chain simple lipids, which may be interpreted as a strategy to maintain membrane fluidity. 14C labeling showed that most of the oleic acid taken up from the medium was incorporated into the membrane fraction of the cells.
A compact single post internal mammary artery dissection retractor (1989)

Considering the ergonomics of an efficient exposure of the retrosternal area, the design of the internal mammary artery dissection retractor resulted in an alternative compact and easy adjustable construction. A single post fixation enables a quick setup and takedown over the sterile drapes in one piece. So, the usual numerous nuts and knobs and different assembly parts are superfluous.