gebhart/patrepeval huggingface dataset:
RE-MIND2: comparative effectiveness of tafasitamab plus lenalidomide versus polatuzumab vedotin/bendamustine/rituximab (pola-BR), CAR-T therapies, and lenalidomide/rituximab (R2) based on real-world data in patients with relapsed/refractory diffuse large B-cell lymphoma (2023)

RE-MIND2 (NCT04697160) compared patient outcomes from the L-MIND (NCT02399085) trial of tafasitamab+lenalidomide with those of patients treated with other therapies for relapsed/refractory (R/R) diffuse large B-cell lymphoma (DLBCL) who are autologous stem cell transplant ineligible. We present outcomes data for three pre-specified treatments not assessed in the primary analysis. Data were retrospectively collected from sites in North America, Europe, and the Asia Pacific region. Patients were aged ≥18 years with histologically confirmed DLBCL and received ≥2 systemic therapies for DLBCL (including ≥1 anti-CD20 therapy). Patients enrolled in the observational and L-MIND cohorts were matched using propensity score-based 1:1 nearest-neighbor matching, balanced for six covariates. Tafasitamab+lenalidomide was compared with polatuzumab vedotin+bendamustine+rituximab (pola-BR), rituximab+lenalidomide (R2), and CD19-chimeric antigen receptor T-cell (CAR-T) therapies. The primary endpoint was overall survival (OS). Secondary endpoints included treatment response and progression-free survival. From 200 sites, 3,454 patients were enrolled in the observational cohort. Strictly matched patient pairs consisted of tafasitamab+lenalidomide versus pola-BR (n = 24 pairs), versus R2 (n = 33 pairs), and versus CAR-T therapies (n = 37 pairs). A significant OS benefit was observed with tafasitamab+lenalidomide versus pola-BR (HR: 0.441; p = 0.034) and R2 (HR: 0.435; p = 0.012). Comparable OS was observed in tafasitamab+lenalidomide and CAR-T cohorts (HR: 0.953, p = 0.892). Tafasitamab+lenalidomide appeared to improve survival outcomes versus pola-BR and R2, and comparable outcomes were observed versus CAR-T. Although based on limited patient numbers, these data may help to contextualize emerging therapies for R/R DLBCL. CLINICAL TRIAL REGISTRATION: NCT04697160 (January 6, 2021).
Temperature Sensitivity and Composition of Nitrate-Reducing Microbiomes from a Full-Scale Woodchip Bioreactor Treating Agricultural Drainage Water (2021)

Denitrifying woodchip bioreactors (WBR), which aim to reduce nitrate (NO<sub>3</sub><sup>-</sup>) pollution from agricultural drainage water, are less efficient when cold temperatures slow down the microbial transformation processes. Conducting bioaugmentation could potentially increase the NO<sub>3</sub><sup>-</sup> removal efficiency during these specific periods. First, it is necessary to investigate denitrifying microbial populations in these facilities and understand their temperature responses. We hypothesized that seasonal changes and subsequent adaptations of microbial populations would allow for enrichment of cold-adapted denitrifying bacterial populations with potential use for bioaugmentation. Woodchip material was sampled from an operating WBR during spring, fall, and winter and used for enrichments of denitrifiers that were characterized by studies of metagenomics and temperature dependence of NO<sub>3</sub><sup>-</sup> depletion. The successful enrichment of psychrotolerant denitrifiers was supported by the differences in temperature response, with the apparent domination of the phylum <i>Proteobacteria</i> and the genus <i>Pseudomonas</i>. The enrichments were found to have different microbiomes' composition and they mainly differed with native woodchip microbiomes by a lower abundance of the genus <i>Flavobacterium</i>. Overall, the performance and composition of the enriched denitrifying population from the WBR microbiome indicated a potential for efficient NO<sub>3</sub><sup>-</sup> removal at cold temperatures that could be stimulated by the addition of selected cold-adapted denitrifying bacteria.
Mycobiota: Micro-Eukaryotes Inhabiting Our Body as Commensals or Opportunistic Pathogens (2015)

The advent of metagenomics has profoundly revolutionized our way to describe microbial communities and discover sequence based biomarkers of health and disease. Similarly to bacteria commensal fungi are an essential part of human ecosystems being involved in the normal development of the immune system and for the maintenance of healthy tissues and physiological processes. More and more frequently patterns of fungal species are associated to immune disorders and increasing evidences are accumulating of the importance to study the co-occurrence of fungal flora and its microbial counterpart to understand the cross-talk between opportunistic fungi and the mammalian host. Here we critically analyze the studies investigating thefungal communities inhabiting ourbody, addressing at what extent the selection of the approaches and the molecular markers used determine the results obtained
Supplementary table s4 from Predicting the Grade of Dysplasia of Pancreatic Cystic Neoplasms Using Cyst Fluid DNA Methylation Markers (2023)

&lt;p&gt;Supplementary Table S4. Combination analysis of preoperative EUS-FNA cytology with methylated markers using 47 cases who underwent preoperative EUS.&lt;/p&gt;
Perfusion electrodeposition of calcium phosphate on rapid prototyped titanium scaffold for bone engineering (2009)

status: Published
Use of Molecular Beacons for Rapid, Real-Time, Quantitative Monitoring of Cytotoxic T-Lymphocyte Epitope Mutations in Simian Immunodeficiency Virus (2005)

Immune pressure on lentiviruses exerted by cytotoxic T lymphocytes (CTL) selects for virus CTL epitope mutations. Currently employed methods for monitoring emerging CTL epitope mutations rely on the labor-intensive and time-consuming techniques of virus population or clonal sequencing. Here we describe the development of a high-throughput quantitative reverse transcription-PCR assay that facilitates large-scale CTL epitope monitoring. This approach utilizes both sequence-specific molecular beacons and the sequence-independent double-stranded DNA binding dye Sybr Green. We show that this assay detects single-nucleotide mutations in an immunodominant CTL epitope in viral RNA isolated from both viral culture supernatants and plasma samples from simian immunodeficiency virus (SIV)-infected rhesus monkeys. Furthermore, mutant viruses can be detected even when they represent as few as 500 mutant copies in a sample containing 10,000 total copies. This real-time PCR technique for evaluating CTL epitope mutations may prove to be a useful tool for monitoring the genetic drift of human immunodeficiency virus and SIV in infected individuals.
Cover Image, Volume 25, Issue 7 (2017)

The cover image, by Tom Borgers et al., is based on the EU PVSEC Paper A woven fabric for interconnecting back-contact solar cells, DOI 10.1002/pip.2851.
Shape Entropy of a Reconfigurable Ising Surface (2022)

Disclinations in a 2D sheet create regions of Gaussian curvature whose inversion produces a reconfigurable surface with many distinct metastable shapes, as shown by molecular dynamics of a disclinated graphene monolayer. This material has a near-Gaussian "density of shapes" and an effectively antiferromagnetic interaction between adjacent cones. A∼10 nm patch has hundreds of distinct metastable shapes with tunable stability and topography on the size scale of biomolecules. As every conical disclination provides an Ising-like degree of freedom, we call this technique "Isigami."
Lymphoma Cell Burden in Progenitor Cell Grafts Measured by Competitive Polymerase Chain Reaction: Less Than One Log Difference Between Bone Marrow and Peripheral Blood Sources (1998)

A controversy persists in autologous transplantation as to which source of progenitor cells, bone marrow (BM) or peripheral blood (PB), contains the lowest number of contaminating lymphoma cells, and how mobilization procedures affect these numbers. To accurately measure the number of non-Hodgkin's lymphoma (NHL) cells harboring the bcl-2/immunoglobulin H (IgH) rearrangement in progenitor cell grafts, we developed a nested quantitative competitive polymerase chain reaction assay (QC-PCR). DNA from lymph nodes of four patients with NHL were cloned into the pSK(+) vectors to generate four internal controls (ICs) (two with major breakpoint region [MBR] and two with minor cluster region [mcr] rearrangements). The kinetics of amplification of ICs paralleled those of bcl-2/IgH rearranged genomic DNA. When used in a QC-PCR assay, these ICs were accurate at a 0.2-log level and provided reproducible results, as shown by low intrarun and interrun variability. An excellent correlation between predicted and observed lymphoma cell content (r = .99) was observed over a range of at least 5 logs of rearranged cells. This approach was used to measure involvement by NHL cells at the time of progenitor cell harvest in 37 autologous transplant patients. The number of bcl-2/IgH rearranged cells in BM, PB, and mobilized PB (mPB) was found to vary from 1 to 1.1 x 10(5) per million cells. The number of lymphoma cells present in BM was significantly higher than in PB (P = .0001), with a median difference in lymphoma cell content between BM and PB of 0.48 log of cells (range, -0.7 to 5 logs). In contrast, we found no difference in the concentration of bcl-2/IgH rearranged cells present in BM versus PB progenitor cells mobilized with cyclophosphamide and granulocyte colony-stimulating factor (G-CSF) (mPB) (P = .57). In conclusion, the QC-PCR assay described in this study could measure accurately and reproducibly the number of bcl-2/IgH rearranged cells among normal cells. Differences in levels of contamination by lymphoma cells between BM and PB were of less than one log (10-fold), and no differences in lymphoma cell concentrations were observed between BM and mobilized PB. As more cells are usually infused with mPB than with BM grafts, mPB progenitor cell grafts may actually be associated with higher levels of contamination by lymphoma cells. Furthermore, this QC-PCR assay should provide an important tool to assess the prognostic impact of lymphoma cell burden both in progenitor cell grafts and in vivo.
Coupling between Cyclooxygenase, Terminal Prostanoid Synthase, and Phospholipase A2 (2001)

We have recently shown that two distinct prostaglandin (PG) E(2) synthases show preferential functional coupling with upstream cyclooxygenase (COX)-1 and COX-2 in PGE(2) biosynthesis. To investigate whether other lineage-specific PG synthases also show preferential coupling with either COX isozyme, we introduced these enzymes alone or in combination into 293 cells to reconstitute their functional interrelationship. As did the membrane-bound PGE(2) synthase, the perinuclear enzymes thromboxane synthase and PGI(2) synthase generated their respective products via COX-2 in preference to COX-1 in both the -induced immediate and interleukin-1-induced delayed responses. Hematopoietic PGD(2) synthase preferentially used COX-1 and COX-2 in the -induced immediate and interleukin-1-induced delayed PGD(2)-biosynthetic responses, respectively. This enzyme underwent stimulus-dependent translocation from the cytosol to perinuclear compartments, where COX-1 or COX-2 exists. COX selectivity of these lineage-specific PG synthases was also significantly affected by the concentrations of arachidonate, which was added exogenously to the cells or supplied endogenously by the action of cytosolic or secretory phospholipase A(2). Collectively, the efficiency of coupling between COXs and specific PG synthases may be crucially influenced by their spatial and temporal compartmentalization and by the amount of arachidonate supplied by PLA(2)s at a moment when PG production takes place.
Screening prostate cancer using a portable near infrared scanning imaging unit with an optical fiber-based rectal probe (2012)

A portable near infrared scanning polarization imaging unit with an optical fiber-based rectal probe, namely Photonic Finger, was designed and developed o locate the 3D position of abnormal prostate site inside normal prostate tissue. An inverse algorithm, Optical Tomography using Independent Component Analysis (OPTICA) was improved particularly to unmix the signal from targets (cancerous tissue) embedded in a turbid medium (normal tissue) in the backscattering imaging geometry. Photonic Finger combined with OPTICA was tested to characterize different target(s) inside different tissue medium, including cancerous prostate tissue embedded by large piece of normal tissue.
Combinatorial methodologies offer potential for rapid research of photoresist materials and formulations (2002)

A combinatorial research methodology is outlined with the potential to investigate material factors in photoresist formulations more rapidly than with traditional experimental design. The approach involves generating a gradient of processing variables in the photoresist film and using a set of analysis tools to “map” the photoresist properties as a function of the gradient variables. While high-throughput strategies have proven useful for empirical optimization of photoresist processing conditions, they have not been fully exploited to probe the complex array of material issues in projection lithography. Of primary importance in combinatorial methodologies is the generation of variable gradients. The focus of this article is to illustrate techniques to generate a gradient in bake temperature and bake time in the polymer films, and to illustrate that these gradient techniques can be used to probe fundamental properties of lithographic materials, such as deprotection kinetics. These gradient techniques were applied to rapidly probe the deprotection behavior of a poly(tertbutyloxy-carbonyloxy-styrene). The deprotection data, obtained by applying the combinatorial gradients, agrees well with previous literature, validating the accuracy of these high throughput methods. The advantage of the combinatorial research strategies lies in the potential to investigate fundamental lithographic phenomena more rapidly than with traditional experimentation.
The application of positron emission tomography to the study of panic disorder (1986)

Positron emission tomography was used to study eight patients with panic disorder who were vulnerable to lactate-induced panic, eight patients with panic disorder who were not vulnerable to lactate-induced panic, and 25 normal control subjects. Patients who were vulnerable to lactate-induced panic had several abnormalities in the resting, nonpanic state: an abnormal hemispheric asymmetry of parahippocampal blood flow, blood volume, and oxygen metabolism; abnormally high whole brain metabolism; and abnormal susceptibility to episodic hyperventilation. A hypothetical model for the neurobiology of panic disorder, involving the abnormal parahippocampal region and its afferent and efferent connections, is proposed.
Effect of High-Temperature Annealed Al2O3 insulator on GaN MIS-HEMTs performance (2022)

We investigated the effects of high-temperature annealed (HTA) at 880 °C of Al2O3 gate insulator on the performance of AlGaN/GaN MIS-HEMTs. HTA-Al2O3 MIS-capacitors exhibited evidences of spillover of 2DEG from AlGaN/GaN to Al2O3/AlGaN interface. Moreover, HTA-Al2O3 MIS-HEMTs also showed smaller hysteresis in transfer curves and higher maximum drain current compared to those of the reference Al2O3/AlGaN/GaN MIS-HEMTs. These suggest highly improved insulator/semiconductor interfaces by high-temperature annealing of Al2O3 insulator layer.
Early Impairment of Insulin Sensitivity, β-Cell Responsiveness, and Insulin Clearance in Youth with Stage 1 Type 1 Diabetes (2021)

Presymptomatic Stage 1 T1D in youth is associated with reduced insulin sensitivity and lower β-cell responsiveness, and the presence of blunted insulin clearance.
Impact of Hemodialysis and Post-Dialysis Period on Granular Activity Levels (2020)

Abstract Background: Physical activity (PA) is typically lower on hemodialysis (HD) days. Albeit intradialytic inactivity is expected, it is unknown whether recovery after HD contributes to low PA. We investigated the impact of HD and post-HD period on granular PA relative to HD timing. Methods: We used baseline data from the HDFIT trial conducted from August 2016 to October 2017. Accelerometry measured PA over one week in patients who received thrice-weekly high-flux HD (vintage 3 to 24 months), were clinically stable, and had no ambulatory limitations. PA was assessed on HD days (0 to ≤24 hours after start HD), first non-HD days (&gt;24 to ≤48 hours after start HD) and second non-HD day (&gt;48 to ≤72 hours after start HD). PA was recorded in blocks/slices: 4 hours during HD, 0 to ≤2 hours post-HD (30 minute slices), and &gt;2 to ≤20 hours post-HD (4.5 hour slices). Blocks/slices of PA were captured at concurrent/parallel times on first/second non-HD days compared to HD days. Results: Among 195 patients (mean age 53±15 years, 71% male), step counts per 24-hours were 3919±2899 on HD days, 5308±3131 on first non-HD days (p&lt;0.001), and 4926±3413 on second non-HD days (p=0.032). During concurrent/parallel times to HD on first and second non-HD days, patients took 1308 and 1128 more steps (both p&lt;0.001). Patients took 276 more steps and had highest rates of steps/hour 2-hours post-HD versus same times on first non-HD days (all p&lt;0.05). Consistent findings were observed on second non-HD days. Conclusions: PA was higher within 2-hours of HD versus same times on non-HD days. Lower PA on HD days was attributable to intradialytic inactivity. The established PA profiles are of importance to the design and development of exercise programs that aim to increase activity during and between HD treatments. Trial Registration: HDFIT was registered 20 April 2016 on ClinicalTrials.gov (NCT02787161) https://clinicaltrials.gov/ct2/show/NCT02787161.
Bounce-Flash Lidar (2021)

We demonstrate a new lidar imaging method called bounce-flash lidar , in which the time-of-flight and intensity of two-bounce returns are used to estimate the depth and reflectance of points which are not illuminated directly.
Distribution of G-Protein-Coupled Receptor (GPCR)135 Binding Sites and Receptor mRNA in the Rat Brain Suggests a Role for Relaxin-3 in Neuroendocrine and Sensory Processing (2004)

G-protein-coupled receptor 135 (GPCR135), a former orphan GPCR also known as SALPR, has recently been shown to be modulated by relaxin-3 (R3). In addition to GPCR135, R3 has been shown to be an agonist for GPCR142 (which is a pseudogene in the rat) and to activate LGR7, which is primarily the receptor for relaxin-1/2. The interaction of R3 with LGR7 has confounded the autoradiographic study of the GPCR135 distribution in the rat CNS due to significant expression of LGR7 in the brain. R3/I5, a chimera of the B-chain of R3 bonded to the A-chain of INSL-5, is a specific GPCR135 agonist which is highly selective for GPCR135 over LGR7. [(125)I]R3/I5 specifically binds to sites on rat brain sections with a pharmacology matching results from membrane preparations of recombinant GPCR135 receptors. Autoradiographic studies show the GPCR135 receptor density is most prominent in areas such as the olfactory bulb, sensory cortex, amygdala, thalamus, paraventricular nucleus, supraoptic nucleus, inferior and superior colliculus. The GPCR135 mRNA distribution generally overlaps the pattern of GPCR135 binding sites shown by autoradiography using [(125)I]R3/I5. The nucleus incertus, which has been implicated in the extrapituitary actions of corticotropin-releasing hormone, is the primary source of R3 in the rat central nervous system and expresses GPCR135 receptors. These binding autoradiography and in situ hybridization data suggest that GPCR135 plays an important role in the central processing of sensory signals in rats, are consistent with a putative role for R3/GPCR135 as modulators of stress responses, and confirm the identity of R3 as the central nervous system ligand for GPCR135.
Phenolics from Chrozophora oblongifolia Aerial Parts as Inhibitors of α-Glucosidases and Advanced Glycation End Products: In-Vitro Assessment, Molecular Docking and Dynamics Studies (2022)

Modern life is associated with low physical activity that leads to the accumulation of fats, gaining more weight, and obesity. Accumulation of fat in the abdomen region contributes to diabetes via insulin resistance and hyperglycemia. Polyphenols are major plant constituents that exert antidiabetic activity through different mechanisms, including radicle scavenging activity, regulation of glucose uptake, and inhibition of fat and polysaccharide hydrolysis in addition to their inhibitory role regarding the formation of advanced glycation end products (AGEs). Chemical investigation of <i>C. oblongifolia</i> aerial parts resulted in the isolation of five major compounds: apeginin-7-O-β-D-glucoside (<b>1</b>), quercetin-3-O-β-D-glucuronic acid (<b>2</b>), quercetin-3-O-β-D-galacturonic acid (<b>3</b>), rutin (<b>4</b>), and 1,3,6-trigalloyl glucose (<b>5</b>). The isolated compounds were tested for their antioxidant and AGEs formation, α-glucosidase, and lipase inhibitory activities. Compound <b>5</b> revealed the highest antioxidant and AGEs inhibitory activity in bovine serum albumin (BSA)-methylglyoxal, BSA-fructose, and arginine-methylglyoxal models. Moreover, it exhibited a potent inhibitory profile on <i>Saccharomyces cerevisiae</i> α-glucosidases compared to the positive control, acarbose. Compound (<b>5</b>) further depicted promising binding affinity and stability towards the human intestinal maltase-glucoamylase α-glucosidases, which is a diabetes-related therapeutic target, through coupled molecular docking and dynamics studies. The obtained results encourage the usage of 1,3,6-trigalloyl glucose in the management of diabetes and its complications. However, detailed in-vivo studies for this compound should be performed.
Thermal-conductivity measurements of GaAs/AlAs superlattices using a picosecond optical pump-and-probe technique (1999)

We present measurements of the lattice thermal conductivity ${\ensuremath{\kappa}}_{\ensuremath{\perp}}$ normal to the interfaces of $(\mathrm{GaAs}{)}_{n}/(\mathrm{AlAs}{)}_{n}$ superlattices with n between 1 and 40 monolayers. The conductivity was measured by an optical pump-and-probe technique in the temperature range of 100 to 375 K. In the experiment, an Al film is deposited onto a superlattice sample, and the rate at which this film cools by conduction into the superlattice is determined. We find a general decrease in ${\ensuremath{\kappa}}_{\ensuremath{\perp}}$ with a reduction of the superlattice period. At 300 K, ${\ensuremath{\kappa}}_{\ensuremath{\perp}}$ of the $(\mathrm{GaAs}{)}_{40}/(\mathrm{AlAs}{)}_{40}$ superlattice is approximately three times less than $\ensuremath{\kappa}$ of bulk GaAs, and ${\ensuremath{\kappa}}_{\ensuremath{\perp}}$ of the $(\mathrm{GaAs}{)}_{1}/(\mathrm{AlAs}{)}_{1}$ superlattice is an order of magnitude less than $\ensuremath{\kappa}$ of bulk GaAs. We discuss the decrease in ${\ensuremath{\kappa}}_{\ensuremath{\perp}}$ compared to the bulk constituents in terms of extrinsic and intrinsic scattering mechanisms.
DISPLACEMENT OF 18F-FALLYPRIDE BINDING WITH HALOPERIDOL IN A WITHIN-SUBJECT DESIGN USING A BETA MICROPROBE (2009)

peer reviewed
All-in-one terahertz taste sensor: integrated electronic and bioelectronic tongues (2023)

All-in-one terahertz taste sensor: integrated electronic and bioelectronic tongues with a multiarray of bioreceptors and sensing materials.