gebhart/patrepeval huggingface dataset:
Review of polymer MEMS micromachining (2015)

The development of polymer micromachining technologies that complement traditional silicon approaches has enabled the broadening of microelectromechanical systems (MEMS) applications. Polymeric materials feature a diverse set of properties not present in traditional microfabrication materials. The investigation and development of these materials have opened the door to alternative and potentially more cost effective manufacturing options to produce highly flexible structures and substrates with tailorable bulk and surface properties. As a broad review of the progress of polymers within MEMS, major and recent developments in polymer micromachining are presented here, including deposition, removal, and release techniques for three widely used MEMS polymer materials, namely SU-8, polyimide, and Parylene C. The application of these techniques to create devices having flexible substrates and novel polymer structural elements for biomedical MEMS (bioMEMS) is also reviewed.
Faculty of 1000 evaluation for Ready-to-use therapeutic food for home-based treatment of severe acute malnutrition in children from six months to five years of age. (2013)

Read the full review for this Faculty Opinions recommended article: Ready-to-use therapeutic food for home-based treatment of severe acute malnutrition in children from six months to five years of age.
Gamma-Glutamyltransferase Fractions in Human Plasma and Bile: Characteristic and Biogenesis (2014)

Total plasma gamma-glutamyltransferase (GGT) activity is a sensitive, non-specific marker of liver dysfunction. Four GGT fractions (b-, m-, s-, f-GGT) were described in plasma and their differential specificity in the diagnosis of liver diseases was suggested. Nevertheless fractional GGT properties have not been investigated yet. The aim of this study was to characterize the molecular nature of fractional GGT in both human plasma and bile. Plasma was obtained from healthy volunteers; whereas bile was collected from patients undergoing liver transplantation. Molecular weight (MW), density, distribution by centrifugal sedimentation and sensitivity to both detergent (deoxycholic acid) and protease (papain) were evaluated. A partial purification of b-GGT was obtained by ultracentrifugation. Plasma b-GGT fraction showed a MW of 2000 kDa and a density between 1.063-1.210 g/ml. Detergent converted b-GGT into s-GGT, whereas papain alone did not produce any effect. Plasma m-GGT and s-GGT showed a MW of 1,000 and 200 kDa, and densities between 1.006-1.063 g/ml and 1.063-1.210 g/ml respectively. Both fractions were unaffected by deoxycholic acid, while GGT activity was recovered into f-GGT peak after papain treatment. Plasma f-GGT showed a MW of 70 kDa and a density higher than 1.21 g/ml. We identified only two chromatographic peaks, in bile, showing similar characteristics as plasma b- and f-GGT fractions. These evidences, together with centrifugal sedimentation properties and immunogold electronic microscopy data, indicate that b-GGT is constituted of membrane microvesicles in both bile and plasma, m-GGT and s-GGT might be constituted of bile-acid micelles, while f-GGT represents the free-soluble form of the enzyme.
PerR controls peroxide- and iron-responsive expression of oxidative stress defense genes in<i>Helicobacter hepaticus</i> (2011)

Chronic intestinal and hepatic colonization with the microaerophilic murine pathogen Helicobacter hepaticus can lead to a range of inflammatory diseases of the lower digestive tract. Colonization is associated with an active cellular immune response and production of oxygen radicals. During colonization, H. hepaticus needs to cope with and respond to oxidative stress, and here we report on the role of the H. hepaticus PerR-regulator (HH0942) in the expression of the peroxidase-encoding katA (HH0043) and ahpC (HH1564) genes. Transcription of katA and ahpC was induced by hydrogen peroxide, and by iron restriction of growth media. This iron- and hydrogen peroxide-responsive regulation of katA and ahpC was mediated at the transcriptional level, from promoters directly upstream of the genes. Inactivation of the perR gene resulted in constitutive, iron-independent high-level expression of the katA and ahpC transcripts and corresponding proteins. Finally, inactivation of the katA gene resulted in increased sensitivity of H. hepaticus to hydrogen peroxide and reduced aerotolerance. In H. hepaticus, iron metabolism and oxidative stress defense are intimately connected via the PerR regulatory protein. This regulatory pattern resembles that observed in the enteric pathogen Campylobacter jejuni, but contrasts with the pattern observed in the closely related human gastric pathogen Helicobacter pylori.
Abstract 1332: High Throughput isolation and expansion of circulating tumor cells (CTCs) from Non-small cell lung cancer (NSCLC) patients for personalized treatments (2019)

Background: Circulating tumor cells (CTCs) have emerged as important blood-based surrogate markers of primary tumors. Current methods for isolation of lung CTCs mostly rely on biomarker dependent antibody-based capture, missing populations that may be stem-like in nature. Results: We have applied the microfluidic Labyrinth device for high throughput, label-free, size-based isolation of CTCs from non-small cell lung cancer patients (NSCLC). The Labyrinth device was optimized and tested for inertial separation of cancer cells using the human lung cancer cell line H1650. The recovery and purity were >82% and >78%, respectively, operating at a flow rate of 2.5 mL/min. Using the biomarker-independent Labyrinth separation device, heterogeneous CTC populations were isolated from metastatic NSCLC patients (n=21). Heterogeneous CTC populations were detected, including CTCs (PanCK+ and CD45-), CTCs expressing EpCAM or Vimentin, and CTCs expressing both markers representing an EMT-like population of CTCs. Using Labyrinth, we were able to isolate CTCs from 100% of patients with an average yield of 180±168 CTCs/mL. Among the captured CTCs, EpCAM- CTCs were significantly more common than EpCAM+ CTCs (115.7 vs. 39.1 CTCs/mL respectively). Cell clusters of 2 or more CTCs were also observed in 95% of patients; 79% of these clusters were negative for EpCAM expression, whereas 35% expressed Vimentin, suggestive of an EMT phenotype. Recovered CTCs from patients with RET, ROS1 and ALK rearranged tumors showed aberrations matching with the primary tumor for each gene using FISH analysis. We have successfully expanded the recovered CTCs from 2 patients and screened for therapeutic targeting. We have found that TPX-0005 might be effective in these patients and would direct them to a clinical trial using this compound. Conclusion: The label-free Labyrinth device demonstrated the capability of collecting recovered CTCs from the device using a continuous processing technique while in a suspension state. This advantage opens the opportunities not only for CTC expansion off-chip, but also for ex-vivo drug testing to direct patient-specific therapies.Citation Format: Mina Zeinali, Maggie Lee, Arthi Nadhan, Anvya Mathur, Wei Huang, Eric Lin, Ramdane Harouaka, Max S. Wicha, Nallasivam Palanisamy, Mathias Hafner, Rishindra Reddy, Gregory P. Kalemkerian, Bryan J. Schneider, Khaled A. Hassan, Nithya Ramnath, Sunitha Nagrath. High Throughput isolation and expansion of circulating tumor cells (CTCs) from Non-small cell lung cancer (NSCLC) patients for personalized treatments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1332.
Pediatric Outcome After Maternal Cancer Diagnosed During Pregnancy (2016)

Obstet Gynecol Surv 2016;71(3):144–146 Among women in whom cancer is diagnosed during pregnancy, factors such as maternal illness, diagnostic tests, cancer treatment, and increased levels of maternal stress can negatively influence fetal development. In this multicenter, prospective case-control study involving 129 children and their matched control subjects, the effects of prenatal exposure to maternal cancer and cancer treatment on general health, prenatal and postnatal growth, cognitive development, and cardiac structure and function were documented.
Supplementary Figure 4 from Ror1 Is a Pseudokinase That Is Crucial for Met-Driven Tumorigenesis (2023)

Supplementary Figure 4 from Ror1 Is a Pseudokinase That Is Crucial for Met-Driven Tumorigenesis
Toward Personalized Medicine: One Chelator for Imaging and Therapy with Lutetium-177 and Actinium-225 (2022)

We report a nonadentate bispidine (3,7-diazabicyclo[3.3.1]nonane) that unveils the potential to bind theranostically relevant radionuclides, including indium-111, lutetium-177, and actinium-225 under mild labeling conditions. This radiopharmaceutical candidate allows the simultaneous application of imaging and treatment (radionuclide theranostics) without changing the type of the bioconjugate; that is, it allows the strong binding to an imaging and a therapeutic radionuclide by the same chelator. Since sophisticated coordination chemistry is required to achieve high thermodynamic and kinetic stability (inertness), it is not surprising that only a few chelators have been reported that are able to strongly bind several radionuclides to a satisfactory extent. Bispidine-derived ligands have proven to be ideal for di- and trivalent metal ions with generally fast complexation kinetics and high <i>in vitro</i> and <i>in vivo</i> stabilities. The presented (radio)complexes are formed under mild conditions (pH 6, <40 °C) and exhibit thermodynamic stability and inertness in human serum comparable to the corresponding DOTA complexes. The bispidine-based complexing agent was conjugated to a peptide, targeting somatostatin type 2 receptors (SSTR2), overexpressed on neuroendocrine tumors. The <sup>177</sup>Lu- and <sup>225</sup>Ac-labeled conjugates were investigated, considering their binding to two different SSTR2-positive cell lines, including the human pancreatic carcinoid tumor (BON-SSTR2+) and the murine pheochromocytoma cell line (MPC). The biodistribution and accumulation pattern in MPC tumor-bearing mice was also evaluated. The Lu<sup>III</sup> and Ac<sup>III</sup> complexes studied show how ligand structures can be optimized in general by extending the denticity and varying the donor set in order to allow for fast complex formation and medically relevant inertness.
Preclinical development of novel small molecule anticancer agents targeted focal adhesion kinase pathway. (2007)

B220 Focal Adhesion Kinase (FAK) is an important survival molecule that is upregulated in a broad range of solid tumors and is expressed at very low levels in normal tissues, creating a therapeutic window and making this protein a highly attractive target for the treatment of cancer, as suggested by our lab and recently by other leading authors in the field. We have identified the key binding partners of FAK and peptides from the binding sites that cause apoptosis in cancer but not normal cells. Based on these findings as well as correlative structural and functional data, we suggest that blocking FAK-protein interactions will lead to apoptosis and tumor cell death. We have well-documented data that targeting FAK-protein interactions is important for cell survival and we have used atomic resolution structural data of specific binding sites to identify small molecule lead compounds. We have screened small molecule libraries and identified several lead compounds that disrupt binding of FAK to key signaling molecules and induce apoptosis in breast, colon, pancreatic, lung, as well as melanoma cancer cell lines. Some of these compounds caused apoptosis at low nanomolar concentrations. We also have shown that lead compounds increase the sensitivity of cancer cells to standard chemotherapy drugs.  Our data suggest that peptides and small molecule inhibitors of FAK-protein interaction can be identified as lead compounds to provide the basis for targeted novel cancer therapeutic agents. Such compounds will effectively reduce activation of both molecules involved in survival signaling and will lead to sensitivity to chemotherapy and cancer cell death. We anticipate that our approach (targeting FAK protein-protein interactions) is amenable to more successful drug discovery and development than the typical method of targeting the kinase activity by targeting ATP binding site of tyrosine kinases. Experience shows that it is especially difficult in the case of FAK due to cross-reactivity with other essential tyrosine kinases.
Differential Ia antigen expression by autologous human erythroid and B lymphoblastoid cell lines. (1985)

Human erythroid precursors express Ia antigens that have serology, function, molecular nature, and genetic regulation that are largely unknown. To approach these issues, Ia+ and Ia- subclones of the HEL human erythroleukemia cell line (HEL-DR+ and HEL-DR-, respectively) and an autologous B lymphoblastoid line (B line) were isolated. These erythroid and lymphoid lines were compared with respect to their binding of monoclonal HLA-D subregion-specific antibodies, the ability to trigger in vitro alloproliferation, expression of class II molecules, and transcription of class II-related genes. Unlike the DP+/DQ+/DR+ B lines, HEL-DR+ differentially expressed DP and DR, but not DQ specificities. Also unlike the autologous B line, HEL-DR+ appeared to be unable to trigger primary or secondary allogeneic T cell proliferation, despite the presence of responder monocytes in these cultures and irrespective of lymphokine addition. HEL-DR+ expression of bona fide class II molecules similar to B line DR heterodimers was verified by two-dimensional gel electrophoresis of material immunoprecipitated from 125I-labeled cells. Northern blot analysis of cytoplasmic RNA from these lines indicated that differential class II gene transcription could readily explain the distinct, lineage-related Ia phenotypes of HEL-DR+ and B line. In addition, the lack of invariant chain and class II transcripts in HEL-DR- implied that expression of these unlinked genes in HEL cells is co-regulated.
Ongoing Prothrombotic State in Patients With Antiphospholipid Antibodies: A Role for Increased Lipid Peroxidation (1999)

We measured the urinary excretion of Isoprostane F2alpha-III and Isoprostane-F2alpha-VI, two markers of in vivo lipid peroxidation, and the circulating levels of the prothrombin fragment F1+2, a marker of thrombin generation, in 18 antiphospholipid antibodies-positive patients, in 18 antiphospholipid antibodies-negative patients with systemic lupus erythematosus, and in 20 healthy subjects. Furthermore, 12 patients positive for antiphospholipid antibodies were treated with (n = 7) or without (n = 5) antioxidant vitamins (vitamin E at 900 IU/d and vitamin C at 2, 000 mg/d) for 4 weeks. Compared with antiphospholipid antibodies-negative patients, antiphospholipid antibodies-positive patients had higher urinary values of Isoprostane-F2alpha-III (P =. 0001), Isoprostane-F2alpha-VI (P =.006), and plasma levels of the prothrombin fragment F1+2 (P =.0001). In antiphospholipid-positive patients, F1+2 significantly correlated with Isoprostane-F2alpha-III (Rho =.56, P =.017) and Isoprostane-F2alpha-VI (Rho =.61, P =.008). After 4 weeks of supplementation with antioxidant vitamins, we found a significant decrease in F1+2 levels (P <.005) concomitantly with a significant reduction of both Isoprostane-F2alpha-III (P =.007) and Isoprostane-F2alpha-VI (P <.005). No change of these variables was observed in patients not receiving antioxidant treatment. This study suggests that lipid peroxidation might contribute to the activation of clotting system in patients positive for antiphospholipid antibodies.
Reshaping connectivity patterns by controlling the collective dynamics of bursting neurons (2008)

Desynchronizing stimulation has a strong impact on the dynamics of a network that features dynamical multistability. In the studied model the dynamical multistability is caused by synaptic plasticity with symmetric spike timing characteristics. Desynchronizing stimuli can reliably shift the network from a stable state with pathological synchrony to a stable desynchronized state. The effect of the desychronizing stimulation is exemplified by a detailed study of a simulation showing such therapeutic effects.
Flexible transducer arrays with through-wafer electrical interconnects based on trench refilling with PDMS (2007)

This paper reports on a method to fabricate flexible onedimensional (1D) and two-dimensional (2D) micromachined transducer arrays that are electrically connected to flip-chip bond pads on the back side of the array. In our case, the transducers are capacitive micromachined ultrasonic transducers (CMUT) intended for medical ultrasound imaging. For ultrasound imaging, flexible arrays conform to the body part being imaged. Flexible arrays are also desired for certain catheter and fixed-focus array geometries. Electrical connection to bond pads on the back side of the array is provided for flip-chip bonding to an integrated circuit or flexible PCB. The arrays are made flexible by etching through-wafer trenches and filling the trenches with polydimethylsiloxane (PDMS). The flexibility of the substrate is demonstrated by wrapping it around a needle tip with a radius of 650 μm (French catheter size of 4).
Recombinant adenovirus expressing wild-type p53 is antiangiogenic: a proposed mechanism for bystander effect. (1999)

Angiogenesis is required for the growth and progression of malignancies. Recent studies have demonstrated that genetic alterations may accompany acquisition of the angiogenic phenotype. The tumor suppressor gene p53 is most frequently mutated in human cancers and is also known to be a transcriptional regulator of a variety of genes. Here, we investigated the antiangiogenic effect of the wild-type p53 (wt-p53) gene transfer on a human non-small cell lung cancer cell line. Mutant p53-expressing H226Br non-small cell lung cancer cells were transduced with the wt-p53 gene using a recombinant adenoviral vector (Ad5CMVp53) and applied to semiquantitative reverse transcription-PCRs for the detection of altered mRNA expression of angiogenic and/or antiangiogenic factors. In vivo neovascularization assay of Ad5CMVp53-infected cells was then performed using a membrane-diffusion chamber system s.c. transplanted in nu/nu mice. We also evaluated the effect of Ad5CMVp53-infected H226Br cells on nontransduced tumor cells in vivo by s.c. inoculating mixture of cells into nu/nu mice. Ad5CMVp53 infection markedly inhibited the expression of an angiogenic factor, vascular endothelial growth factor, and increased the expression of a novel antiangiogenic factor, brain-specific angiogenesis inhibitor 1, resulting in reduced neovascularization in vivo. Mixing experiments showed that tumor cells transduced with the wt-p53 gene inhibited the in vivo tumor growth of adjacent nontransduced cells. Our data suggest that a recombinant adenovirus expressing the wt-p53 gene is antiangiogenic, which may explain, in part, the mechanism of the bystander effect induced by the wt-p53 gene transfer on adjacent tumor cells.
Mehrkanaliges akustisches Front-End für Spracherkennungssysteme (2009)

Mehrmikrofonanordnungen erweitern die Moglichkeiten der
Vorverarbeitung von Audiosignalen fur die Spracherkennung. Sie ermoglichen die
Nutzung von Beamforming-Algorithmen, mit deren Hilfe Storgerausche und
Raumeinflusse reduziert werden konnen. In diesem Beitrag werden verschiedene
Beamformer vorgestellt und deren Vor- und Nachteile fur die Spracherkennung
diskutiert. Es wurden Messungen in praktisch relevanten Umgebungen
vorgenommen, deren Auswirkung auf die Erkennungsrate hier gezeigt werden. Des
Weiteren erfolgt die Vorstellung eines aktuellen Projektes des Institut fur Akustik
und Sprachkommunikation der TU Dresden mit mehreren Partnern zur Entwicklung
eines public Terminals mit robuster Spracherkennung.
Nuclear Magnetic Resonance Studies of Vortices in High Temperature Superconductors (2011)

The distinct distribution of local magnetic fields due to superconducting vortices can be detected with nuclear magnetic resonance (NMR) and used to investigate vortices and related physical properties of extreme type II superconductivity. This review summarizes work on high temperature superconductors (HTS) including cuprates and pnictide materials. Recent experimental results are presented which reveal the nature of vortex matter and novel electronic states. For example, the NMR spectrum has been found to provide a sharp indication of the vortex melting transition. In the vortex solid a frequency dependent spin-lattice relaxation has been reported in cuprates, including YBa$_2$Cu$_3$O$_{7-x}$, Bi$_2$SrCa$_2$Cu$_2$O$_{8+δ}$, and Tl$_2$Ba$_2$CuO$_{6+δ}$. These results have initiated a new spectroscopy via Doppler shifted nodal quasiparticles for the investigation of vortices. At very high magnetic fields this approach is a promising method for the study of vortex core excitations. These measurements have been used to quantify an induced spin density wave near the vortex cores in Bi$_2$SrCa$_2$Cu$_2$O$_{8+δ}$. Although the cuprates have a different superconducting order parameter than the iron arsenide superconductors there are, nonetheless, some striking similarities between them regarding vortex dynamics and frequency dependent relaxation.
Stereoselective Synthesis and Retentive Trapping of α‐Chiral Secondary Alkyllithiums Leading to Stereodefined α,β‐Dimethyl Carboxylic Esters (2016)

The treatment of α-chiral secondary alkyl iodides with tBuLi at -100 °C leads to the corresponding secondary alkyllithiums with high retention of configuration. Subsequent quenching with various electrophiles such as Bu2 S2 , DMF, MeOB(OR)2 , or Et2 CO provides the desired products with retention of configuration. Furthermore, a transmetalation with CuBr⋅P(OEt)3 also allows retentive trapping with acid chlorides and ethylene oxide. The quenching of the resulting alkyllithiums with ClCO2 Et furnishes stereoselectively syn- and anti-ethyl-2,3-dimethyl ester carboxylates (d.r.>94 %). Related esters bearing three adjacent stereo-controlled centers (stereotriads) have also been prepared. This method has been applied to the synthesis of the ant pheromone (±)-lasiol in 26 % overall yield (four steps) with d.r.=97:3 starting from commercially available cis-2,3-epoxybutane.
Translation on this Article from γH2AX Expression in Tumors Exposed to Cisplatin and Fractionated Irradiation (2023)

Translation on this Article from γH2AX Expression in Tumors Exposed to Cisplatin and Fractionated Irradiation
Influence of oxygen on surface morphology of metalorganic vapor phase epitaxy grown GaAs (001) (1996)

Atomic force microscopy has been used to investigate the influence of controlled oxygen incorporation on the surface morphology of GaAs films grown by metalorganic vapor phase epitaxy (MOVPE). Oxygen influences the periodic morphology observed in GaAs surfaces, with concentrations about 1018 cm−3 leading to a breakup of the periodicity. To account for these observations, we propose a model in which oxygen preferentially attaches at steps with a subsequent reduction in step mobility and a concomitant increase in the surface roughness.