gebhart/patrepeval huggingface dataset:
Ex Vivo–expanded Natural Killer Cells Demonstrate Robust Proliferation In Vivo in High-risk Relapsed Multiple Myeloma Patients (2014)

Highly activated/expanded natural killer (NK) cells can be generated by stimulation with the human leukocyte antigen-deficient cell line K562, genetically modified to express 41BB-ligand and membrane-bound interleukin (IL)15. We tested the safety, persistence, and activity of expanded NK cells generated from myeloma patients (auto-NK) or haploidentical family donors (allo-NK) in heavily pretreated patients with high-risk relapsing myeloma. The preparative regimen comprised bortezomib only or bortezomib and immunosuppression with cyclophosphamide, dexamethasone, and fludarabine. NK cells were shipped overnight either cryopreserved or fresh. In 8 patients, up to 1×10⁸ NK cells/kg were infused on day 0 and followed by daily administrations of IL2. Significant in vivo expansion was observed only in the 5 patients receiving fresh products, peaking at or near day 7, with the highest NK-cell counts in 2 subjects who received cells produced in a high concentration of IL2 (500 U/mL). Seven days after infusion, donor NK cells comprised >90% of circulating leukocytes in fresh allo-NK cell recipients, and cytolytic activity against allogeneic myeloma targets was retained in vitro. Among the 7 evaluable patients, there were no serious adverse events that could be related to NK-cell infusion. One patient had a partial response and in another the tempo of disease progression decreased; neither patient required further therapy for 6 months. In the 5 remaining patients, disease progression was not affected by NK-cell infusion. In conclusion, infusion of large numbers of expanded NK cells was feasible and safe; infusing fresh cells was critical to their expansion in vivo.
Nonhomologous chromosomal integration of foreign DNA is completely dependent on MUS-53 (human Lig4 homolog) in Neurospora (2006)

Homologous integration of a foreign DNA segment into a chromosomal target sequence enables precise disruption or replacement of genes of interest and provides an effective means to analyze gene function. However, integration after transformation is predominantly nonhomologous in most species other than yeast. Here, we show that homologous integration in the filamentous fungus Neurospora requires the homologous-recombination proteins MEI-3 (yeast Rad51 homolog) and MUS-25 (yeast Rad54 homolog), whereas nonhomologous integration requires nonhomologous end-joining protein MUS-52 (yeast Ku80 homolog). Two additional minor integration pathways are present, one MEI-3-independent and homologous, the other MUS-52-independent and nonhomologous. Homologous and nonhomologous mechanisms compete when external DNA is integrated. In Neurospora, both nonhomologous integration pathways, MUS-52-dependent and MUS-52-independent, require MUS-53 (a homolog of human Lig4), which functions in the final step of nonhomologous end-joining. Because nonhomologous integration is eliminated in a LIG4-disrupted strain, integration occurs only at the targeted site in mus-53 mutants, making them an extremely efficient and safe host for gene targeting.
Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems (2012)

The human gut microbiota comprise a complex and dynamic ecosystem that profoundly affects host development and physiology. Standard approaches for analyzing time-series data of the microbiota involve computation of measures of ecological community diversity at each time-point, or measures of dissimilarity between pairs of time-points. Although these approaches, which treat data as static snapshots of microbial communities, can identify shifts in overall community structure, they fail to capture the dynamic properties of individual members of the microbiota and their contributions to the underlying time-varying behavior of host ecosystems. To address the limitations of current methods, we present a computational framework that uses continuous-time dynamical models coupled with Bayesian dimensionality adaptation methods to identify time-dependent signatures of individual microbial taxa within a host as well as across multiple hosts. We apply our framework to a publicly available dataset of 16S rRNA gene sequences from stool samples collected over ten months from multiple human subjects, each of whom received repeated courses of oral antibiotics. Using new diversity measures enabled by our framework, we discover groups of both phylogenetically close and distant bacterial taxa that exhibit consensus responses to antibiotic exposure across multiple human subjects. These consensus responses reveal a timeline for equilibration of sub-communities of micro-organisms with distinct physiologies, yielding insights into the successive changes that occur in microbial populations in the human gut after antibiotic treatments. Additionally, our framework leverages microbial signatures shared among human subjects to automatically design optimal experiments to interrogate dynamic properties of the microbiota in new studies. Overall, our approach provides a powerful, general-purpose framework for understanding the dynamic behaviors of complex microbial ecosystems, which we believe will prove instrumental for future studies in this field.
Tighter Variational Bounds are Not Necessarily Better (2018)

We provide theoretical and empirical evidence that using tighter evidence lower bounds (ELBOs) can be detrimental to the process of learning an inference network by reducing the signal-to-noise ratio of the gradient estimator. Our results call into question common implicit assumptions that tighter ELBOs are better variational objectives for simultaneous model learning and inference amortization schemes. Based on our insights, we introduce three new algorithms: the partially importance weighted auto-encoder (PIWAE), the multiply importance weighted auto-encoder (MIWAE), and the combination importance weighted auto-encoder (CIWAE), each of which includes the standard importance weighted auto-encoder (IWAE) as a special case. We show that each can deliver improvements over IWAE, even when performance is measured by the IWAE target itself. Furthermore, our results suggest that PIWAE may be able to deliver simultaneous improvements in the training of both the inference and generative networks.
Particle Segregation and Dynamics in Confined Flows (2009)

Nonlinearity in finite-Reynolds-number flow results in particle migration transverse to fluid streamlines, producing the well-known "tubular pinch effect" in cylindrical pipes. Here we investigate these nonlinear effects in highly confined systems where the particle size approaches the channel dimensions. Experimental and numerical results reveal distinctive dynamics, including complex scaling of lift forces with channel and particle geometry. The unique behavior described in this Letter has broad implications for confined particulate flows.
Dissecting the individuality of cancer cells: The morphological and molecular dynamics of single human glioma cells (1996)

A glioma produces some of the most heterogeneously growing, angiogenic, and invasive primary brain tumor cells known. To dissect cellular individuality, and therefore tumor heterogeneity, multiple morphological and molecular processes in single living human glioma cells were measured using multimode light microscopy. Feature extraction of time-lapse image series of spreading, locomoting, and interacting cells either in the presence or absence of physiological modulators was performed by defining five parameters that described cell shape, movement, and cell-cell contacts. Concurrent visualization of all five parameters with a scatterplot matrix revealed temporal as well as time-independent relationships between the parameters that were sufficient to define the individuality of normal and transformed glial cells. Because the actin-cytoskeleton plays a role in regulating the cellular processes described above, the dynamics of a fluorescent analog of non-muscle actin within motile glioma cells were measured in addition to the morphological parameters. The actin-cytoskeleton within the thin sweeping lamellipodia of a glioma exhibited a paucity of large stress fibers, a rich collection of microvillar structures containing actin, and dynamics that were distinct from those of normal motile cells. This approach can therefore potentially be used to dissect the molecular origins of transformation using a small number of representative tumor cells. © 1996 Wiley-Liss, Inc.
Synthesis of poly-L-glutamates containing 5-substituted uracil moieties. (1985)

The polymer reaction of cyclic derivatives of uracil and 5-bromouracil with polyacrylic and polymethacrylic acids, and poly-L-glutamic acid was studied in dimethylformamide solution. A similar reaction of cyclic derivatives of uridine with the polymeric acids was also made. Alkaline hydrolysis was further carried out on the polymers obtained.
Mass Spectra of Some 1,2,4-Triazoles (1991)

Abstract The electron-impact induced fragmentation of some 4,5-dihydro-1,2,4-triazole derivatives was studied by conventional mass spectrometry. Some major fragment ions observed in the spectra were interpreted and fragmentation patterns involving McLafferty rearrangements were proposed.
Molecular Detection of the ETV6-NTRK3 Gene Fusion Differentiates Congenital Fibrosarcoma From Other Childhood Spindle Cell Tumors (2000)

Congenital fibrosarcoma (CFS) is a pediatric spindle cell tumor of the soft tissues that usually presents before the age of 2 years. Although these tumors display histologic features of malignancy and frequently recur, they have a relatively good prognosis and only rarely metastasize. CFS must therefore be differentiated from more aggressive spindle cell sarcomas that occur during childhood, particularly adult-type fibrosarcoma (ATFS), which can have an identical morphology. CFS must also be distinguished from benign but cellular fibroblastic lesions of the same age group, including infantile fibromatosis (IFB) and myofibromatosis (MFB). Unfortunately, standard pathologic examination often does not differentiate CFS from these other conditions. The authors recently identified a novel chromosomal translocation in CFS, t(12;15)(p13;q25), which gives rise to an ETV6-NTRK3 gene fusion. They subsequently developed reverse transcription-polymerase chain reaction (RT-PCR) assays that can detect ETV6-NTRK3 fusion transcripts in CFS frozen or paraffin-embedded tumor specimens. To confirm the use of this assay in the differential diagnosis of CFS, they have screened a larger series of childhood pediatric spindle cell lesions for ETV6-NTRK3 gene fusions, including 11 cases of CFS, 13 malignant spindle cell tumors (including ATFS), and 38 benign spindle cell tumors (including IFB and MFB). Of the 11 cases diagnosed as CFS, 10 showed the ETV6-NTRK3 gene fusion, whereas none of the 51 other malignant or benign spindle cell tumors demonstrated this fusion gene. They also compared their RT-PCR findings with those of conventional cytogenetics and with immunohistochemical detection of the ETV6-NTRK3 protein using antisera to NTRK3. They conclude that RT-PCR analysis is superior to these techniques for the detection of the ETV6-NTRK3 gene fusion in pediatric spindle cell tumors, and it is a reliable and specific modality for the diagnosis of CFS.
Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling (2017)

Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological processes. Affinity purification coupled to mass spectrometry (AP-MS) has become the method of choice for identifying protein-protein interactions. However, conventional AP-MS studies provide information on protein interactions, but the organizational information is lost. To address this issue, we developed a strategy to unravel the distinct functional assemblies a protein might be involved in, by resolving affinity-purified protein complexes prior to their characterization by mass spectrometry. Protein complexes isolated through affinity purification of a bait protein using an epitope tag and competitive elution are separated through blue native electrophoresis. Comparison of protein migration profiles through correlation profiling using quantitative mass spectrometry allows assignment of interacting proteins to distinct molecular entities. This method is able to resolve protein complexes of close molecular weights that might not be resolved by traditional chromatographic techniques such as gel filtration. With little more work than conventional AP-geLC-MS/MS, we demonstrate this strategy may in many cases be adequate for obtaining protein complex topological information concomitantly to identifying protein interactions.
Piezoelectric energy harvesting: State-of-the-art and challenges (2014)

Piezoelectric energy harvesting has attracted wide attention from researchers especially in the last decade due to its advantages such as high power density, architectural simplicity, and scalability. As a result, the number of studies on piezoelectric energy harvesting published in the last 5 years is more than twice the sum of publications on its electromagnetic and electrostatic counterparts. This paper presents a comprehensive review on the history and current state-of-the art of piezoelectric energy harvesting. A brief theory section presents the basic principles of piezoelectric energy conversion and introduces the most commonly used mechanical architectures. The theory section is followed by a literature survey on piezoelectric energy harvesters, which are classified into three groups: (i) macro- and mesoscale, (ii) MEMS scale, and (iii) nanoscale. The size of a piezoelectric energy harvester affects a variety of parameters such as its weight, fabrication method, achievable power output level, and potential application areas. Consequently, size-based classification provides a reliable and effective basis to study various piezoelectric energy harvesters. The literature survey on each scale group is concluded with a summary, potential application areas, and future directions. In a separate section, the most prominent challenges in piezoelectric energy harvesting and the studies focusing on these challenges are discussed. The conclusion part summarizes the current standing of piezoelectric energy harvesters as possible candidates for various applications and discusses the issues that need to be addressed for realization of practical piezoelectric energy harvesting devices.
Stress Reduction of Electrodeposited Nickel (1952)

Tests were conducted to investigate possibilities of electroforming low‐stress nickel microwave plumbing. Two methods were studied: use of saccharin as an addition agent in a standard Watts bath, and superimposition of alternating current on direct current. Saccharin reduces stress in nickel deposited from the Watts bath; however, it is unstable, provides erratic results, and is difficult to control. Superimposing alternating current on direct current reduces stress considerably in nickel deposited from the Watts bath. Results verify and extend findings of previous investigations showing that stresses as low as 2,000 psi can be obtained by superimposing 60‐cycle alternating current on direct current in Watts bath.
On the influence of phase noise induced ICI in MIMO OFDM systems (2005)

The influence of transmitter and receiver phase noise (PN) on the performance of a multiple-input multiple-output orthogonal frequency division multiplexing (MIMO OFDM) based communication system is analyzed. It is shown that in the case of frequency flat Rayleigh fading, the influence of receiver and transmitter PN is equal. In the case of independent Rayleigh fading, however, the impact of the receiver PN is shown to depend on the ratio between the number of transmit and receive branches.
Extrapituitary expression of the rat V1b vasopressin receptor gene. (1995)

[Arg8]vasopressin (AVP) stimulates adrenocorticotropic hormone release from the anterior pituitary by acting on the V1b AVP receptor. This receptor can be distinguished from the vascular/hepatic V1a and renal V2 AVP receptors by its differential binding affinities for structural analogous of AVP. Recent studies have shown that the cloned V1a and V2 receptors are structurally related. We have isolated a clone encoding the V1b receptor from a rat pituitary cDNA library using polymerase chain reaction (PCR)-based methodology. The rat V1b receptor is a protein of 421 amino acids that has 37-50% identity with the V1a and V2 receptors. Homology is particularly high in the seven putative membrane-spanning domains of these guanine nucleotide-binding protein-coupled receptors. Expression of the recombinant receptor in mammalian cells shows the same binding specificity for AVP agonists and antagonists as the rat pituitary V1b receptor. AVP-stimulated phosphotidylinositol hydrolysis and intracellular Ca2+ mobilization in Chinese hamster ovary or COS-7 cells expressing the cloned receptor suggest second messenger signaling through phospholipase C. RNA blot analysis, reverse transcription PCR, and in situ hybridization studies reveal that V1b receptor mRNA is expressed in the majority of pituitary corticotropes as well as in multiple brain regions and a number of peripheral tissues, including kidney, thymus, heart, lung, spleen, uterus, and breast. Thus, the V1b receptor must mediate some of the diverse biological effects of AVP in the pituitary as well as other organs.
High Density Lipoproteins (HDL) Interrupt the Sphingosine Kinase Signaling Pathway (1999)

The ability of high density lipoproteins (HDL) to inhibit cytokine-induced adhesion molecule expression has been demonstrated in their protective function against the development of atherosclerosis and associated coronary heart disease. A key event in atherogenesis is endothelial activation induced by a variety of stimuli such as tumor necrosis factor-alpha (TNF), resulting in the expression of various adhesion proteins. We have recently reported that sphingosine 1-phosphate, generated by sphingosine kinase activation, is a key molecule in mediating TNF-induced adhesion protein expression. We now show that HDL profoundly inhibit TNF-stimulated sphingosine kinase activity in endothelial cells resulting in a decrease in sphingosine 1-phosphate production and adhesion protein expression. HDL also reduced TNF-mediated activation of extracellular signal-regulated kinases and NF-kappaB signaling cascades. Furthermore, HDL enhanced the cellular levels of ceramide which in turn inhibits endothelial activation. Thus, the regulation of sphingolipid signaling in endothelial cells by HDL provides a novel insight into the mechanism of protection against atherosclerosis.
A Comparative Study of 20% Azelaic Acid Cream Monotherapy versus a Sequential Therapy in the Treatment of Melasma in Dark-Skinned Patients (2002)

A sequential therapy of topical potent steroids +20% AZA cream can be considered as another alternative treatment for melasma, which combines the beneficial effects of both besides perhaps increasing the compliance of the patients. 20% AZA monotherapy itself is also an effective and well-tolerated therapy for melasma in dark-skinned races.
Fabrication of optical MEMS in sol-gel materials (2003)

A method for fabricating optical MEMS in sol-gel-materials is presented. The basic process involves deposition and patterning of a sacrificial spacer layer and a combined molding and photolithography step. The method described allows the fabrication of micromechanical elements incorporating micro-optical structures such as lenses (diffractive or refractive), gratings (for polarizers or resonant filters), waveguides or other micro-optical relief structures fabricated by UV-curing replication processes.
Antithrombin III: Associations with Age, Race, Sex and Cardiovascular Disease Risk Factors (1994)

Antithrombin III (AT III) is a major inhibitor of blood coagulation, and hereditary deficiency is associated with venous thrombotic disease. The Atherosclerosis Risk in Communities (ARIC) Study, a prospective study of 15,800 middle-aged men and women, measured AT III in its baseline examination. AT III levels were significantly higher in women than men, and in blacks than whites. AT III decreased with age in men but increased with age in women. In age- and race-adjusted analyses, AT III was positively associated with smoking, HDL-cholesterol, triglycerides (men only), and in women, with diabetes and lipoprotein(a). AT III was negatively associated with educational level, body mass index in men, and use of female hormones in women. Most of these associations were confirmed in multivariate analysis. These correlations between AT III and other risk factors must be considered when evaluating AT III as a risk factor for venous or arterial thrombosis.
Potent Immunity to Low Doses of Influenza Vaccine by Probabilistic Guided Micro-Targeted Skin Delivery in a Mouse Model (2010)

Our results represent a marked improvement--an order of magnitude greater than reported by others--for injected doses administered by other delivery methods, without reliance on an added adjuvant, and with only a single vaccination. This study provides a proven mathematical/engineering delivery device template for extension into human studies--and we speculate that successful translation of these findings into humans could uniquely assist with problems of vaccine shortages and distribution--together with alleviating fear of the needle and the need for trained practitioners to administer vaccine, e.g., during an influenza pandemic.
Nonfluoroscopic Transseptal Catheterization: (1998)

Both ICE catheters used in this trial allowed for excellent visualization of the fossa ovalis and safe transseptal puncture. Intracardiac echocardiography may be a better imaging modality than fluoroscopy for guiding transseptal catheterization, especially in less experienced hands.
Protective Effects of α-Tocopherol Against Gentamicin-induced Oto-vestibulo Toxicity: An Experimental Study (2003)

This study supports the hypothesis that alpha-tocopherol interferes with gentamicin-induced free radical formation, and suggests that this drug may be useful in preventing aminoglycoside oto-vestibulo toxicity.
A human homolog of Drosophila warts tumor suppressor, h‐warts, localized to mitotic apparatus and specifically phosphorylated during mitosis (1999)

We identified a human homolog of Drosophila warts tumor suppressor gene, termed h-warts, which was mapped at chromosome 6q24-25.1. The h-warts protein has a serine/threonine kinase domain and is localized to centrosomes in interphase cells. However, it becomes localized to the mitotic apparatus, including spindle pole bodies, mitotic spindle, and midbody, in a highly dynamic manner during mitosis. Furthermore, h-warts is specifically phosphorylated in cells at mitotic phase, most likely by Cdc2 kinase. These findings suggest that h-warts functions as a component of the mitotic apparatus and is involved in proper progression of mitosis.
The influence of clonidine on oral ketamine-midazolam premedication in intellectually disabled patients indicated for dental procedures: double-blind comparison of two sedation regimes. (2012)

Our study is the first to document that oral administration of ketamine and midazolam in low doses represents a safe and effective method of premedication in intellectually disabled patients indicated for dental procedures. Clonidine co-administration did not exert any substantial benefit and should be left out in this clinical setting.