gebhart/patrepeval huggingface dataset:
Two phases of disulfide bond formation have differing requirements for oxygen (2013)

Most proteins destined for the extracellular space require disulfide bonds for folding and stability. Disulfide bonds are introduced co- and post-translationally in endoplasmic reticulum (ER) cargo in a redox relay that requires a terminal electron acceptor. Oxygen can serve as the electron acceptor in vitro, but its role in vivo remains unknown. Hypoxia causes ER stress, suggesting a role for oxygen in protein folding. Here we demonstrate the existence of two phases of disulfide bond formation in living mammalian cells, with differential requirements for oxygen. Disulfide bonds introduced rapidly during protein synthesis can occur without oxygen, whereas those introduced during post-translational folding or isomerization are oxygen dependent. Other protein maturation processes in the secretory pathway, including ER-localized N-linked glycosylation, glycan trimming, Golgi-localized complex glycosylation, and protein transport, occur independently of oxygen availability. These results suggest that an alternative electron acceptor is available transiently during an initial phase of disulfide bond formation and that post-translational oxygen-dependent disulfide bond formation causes hypoxia-induced ER stress.
N-AlGaN Free Deep-Ultraviolet Light-Emitting Diode with Transverse Electron Injection (2023)

For the first time, the n-AlGaN free deep-ultraviolet light-emitting diode (DUV-LED) with transverse electron injection by selective area regrowth (SAG) n+-GaN is demonstrated. The multiple quantum wells (MQWs) and upper layers of the transverse structure LEDs that deposited directly on the AlN template exhibit lower threading dislocation density and better surface morphology compared to conventional structure LEDs with thick n-AlGaN layer. The internal quantum efficiency of the transverse structure LED estimated by temperature-dependent photoluminescence is 95%, which is almost twice higher than that of the conventional structure LED (48%). The electroluminescence intensity of transverse structure LEDs is more than twice that of the conventional structure LEDs. Furthermore, the high crystal quality of MQWs enables transverse structure LEDs to emit shorter peak wavelengths (251–254 nm) and narrower full width at half maximums (10.1–10.7 nm). This study demonstrates that by adopting SAG n+-GaN as an electron injection layer, the n-AlGaN free transverse structure LEDs can be realized, enabling a substantial improvement in DUV-LEDs that are generally based on poor crystal quality n-AlGaN.
The Hypothalamic Neuropeptide Melanin-Concentrating Hormone Acts in the Nucleus Accumbens to Modulate Feeding Behavior and Forced-Swim Performance (2005)

Melanin-concentrating hormone (MCH) is a hypothalamic neuropeptide with a prominent role in feeding and energy homeostasis. The rodent MCH receptor (MCH1R) is highly expressed in the nucleus accumbens shell (AcSh), a region that is important in the regulation of appetitive behavior. Here we establish a role for MCH and MCH1R in mediating a hypothalamic-limbic circuit that regulates feeding and related behaviors. Direct delivery of an MCH1R receptor antagonist to the AcSh blocked feeding and produced an antidepressant-like effect in the forced swim test, whereas intra-AcSh injection of MCH had the opposite effect. Expression studies demonstrated that MCH1R is present in both the enkephalin- and dynorphin-positive medium spiny neurons of the AcSh. Biochemical analysis in AcSh explants showed that MCH signaling blocks dopamine-induced phosphorylation of the AMPA glutamate receptor subunit GluR1 at Ser845. Finally, food deprivation, but not other stressors, stimulated cAMP response element-binding protein-dependent pathways selectively in MCH neurons of the hypothalamus, suggesting that these neurons are responsive to a specific set of physiologically relevant conditions. This work identifies a novel hypothalamic-AcSh circuit that influences appetitive behavior and mediates the antidepressant activity of MCH1R antagonists.
The A3 adenosine receptor agonist CF102 induces apoptosis of hepatocellular carcinoma via de-regulation of the Wnt and NF-κB signal transduction pathways (1992)

The A3 adenosine receptor (A3AR) is highly expressed in tumors and was suggested as a target for cancer treatment. In this study, we show that A3AR is highly expressed in tumor tissues and in peripheral blood mononuclear cells (PBMCs) derived from patients with HCC, as well as from HCC tumor-bearing rats. The high expression level of the receptor was directly correlated to overexpression of NF-κB, known as a transcription factor of A3AR. CF102, a synthetic highly selective agonist to A3AR induced a marked dose response inhibition of tumor growth in N1S1 HCC tumor rats, via de-regulation of the NF-κB and the Wnt signal transduction pathways, resulting in apoptosis of tumor cells. Taken together, A3AR is highly expressed in tumors and PBMCs of HCC patients and tumor-bearing rats. CF102 induced apoptosis and tumor growth inhibition. These data suggest A3AR as a novel targeted therapy to treat HCC.
BLOOMING MECHANISM OF FRESHWATER RED-TIDE IN EUTRORHIC ABOLISHED-RIVER (2011)

This paper analyzes blooming mechanism of freshwater red-tide in an abolished-river which eutrophicated by seventy-years. Outbreaks of red tide of the river is depend on two phenomenon; the first one is the effect of secondary current generated by the wind along with the temperature rise, the second is the flow for the downstream by the release discharge from the power generation-dam in the downstream. Euglena spp. in euglena and Uroglena spp. in yellow-zooxanthellas is clarified to be the dominant species of the freshwater red-tide.
Improvement of the Performances of a Gas-Inducing System for Application in Wastewater Treatment (2006)

Turboxal, a mixing system used for the oxygenation and the mixing of wastewater biological treatment tanks previously studied, shows a low gas flooding rate. In order to increase the gas flooding rate, two of the three impellers used are replaced by only one new turbine. This new turbine comes from a previous work and has been designed partially by computational fluid dynamics (CFD). The gas flooding rate of the new system, called Turboxal-2, is increased of about 120% on average compared to the Turboxal standard and the mass transfer capacities of the new system are quite similar to those of the previous device.
Amyloid pathology but notAPOEε4 status is permissive for tau-related hippocampal dysfunction (2021)

We investigated whether the impact of tau-pathology on memory performance and on hippocampal/medial temporal memory function in non-demented individuals depends on the presence of amyloid pathology, irrespective of diagnostic clinical stage. We conducted a cross-sectional analysis of the observational, multicentric DZNE-Longitudinal Cognitive Impairment and Dementia Study (DELCODE). Two hundred and thirty-five participants completed task functional MRI and provided CSF (92 cognitively unimpaired, 100 experiencing subjective cognitive decline and 43 with mild cognitive impairment). Presence (A+) and absence (A-) of amyloid pathology was defined by CSF amyloid-β42 (Aβ42) levels. Free recall performance in the Free and Cued Selective Reminding Test, scene recognition memory accuracy and hippocampal/medial temporal functional MRI novelty responses to scene images were related to CSF total-tau and phospho-tau levels separately for A+ and A- individuals. We found that total-tau and phospho-tau levels were negatively associated with memory performance in both tasks and with novelty responses in the hippocampus and amygdala, in interaction with Aβ42 levels. Subgroup analyses showed that these relationships were only present in A+ and remained stable when very high levels of tau (>700 pg/ml) and phospho-tau (>100 pg/ml) were excluded. These relationships were significant with diagnosis, age, education, sex, assessment site and Aβ42 levels as covariates. They also remained significant after propensity score based matching of phospho-tau levels across A+ and A- groups. After classifying this matched sample for phospho-tau pathology (T-/T+), individuals with A+/T+ were significantly more memory-impaired than A-/T+ despite the fact that both groups had the same amount of phospho-tau pathology. ApoE status (presence of the E4 allele), a known genetic risk factor for Alzheimer's disease, did not mediate the relationship between tau pathology and hippocampal function and memory performance. Thus, our data show that the presence of amyloid pathology is associated with a linear relationship between tau pathology, hippocampal dysfunction and memory impairment, although the actual severity of amyloid pathology is uncorrelated. Our data therefore indicate that the presence of amyloid pathology provides a permissive state for tau-related hippocampal dysfunction and hippocampus-dependent recognition and recall impairment. This raises the possibility that in the predementia stage of Alzheimer's disease, removing the negative impact of amyloid pathology could improve memory and hippocampal function even if the amount of tau-pathology in CSF is not changed, whereas reducing increased CSF tau-pathology in amyloid-negative individuals may not proportionally improve memory function.
40-Gb/s circuits built from a 120-GHz f/sub T/ SiGe technology (2002)

Product designs for 40-Gb/s applications fabricated from SiGe BiCMOS technologies are now becoming available. In this paper we first briefly discuss heterojunction bipolar transistor (HBT) device operation at high speed, demonstrating that perceived concerns regarding lower BV/sub CEO/ and higher current densities required to operate silicon HBTs at such high speeds do not in actuality limit design or performance. The high-speed portions of the 40-Gb/s system are then addressed individually. We demonstrate the digital capability through a 4: 1 multiplexer and a 1 : 4 demultiplexer running over 50 Gb/s error free at a -3.3-V power supply. We also demonstrate a range of analog elements, including a lumped limiting amplifier which operates with a 35-GHz bandwidth, a transimpedance amplifier with 220-/spl Omega/ gain and 49.1-GHz bandwidth, a 21.5-GHz voltage-controlled oscillator with over -100-dBc/Hz phase noise at 1-MHz offset, and a modulator driver which runs a voltage swing twice the BV/sub CEO/ of the high-speed SiGe HBT. These parts demonstrate substantial results toward product offerings, on each of the critical high-speed elements of the 40-Gb/s system.
High sensitivity transition-tuned long period grating for label-free immunosensing (2010)

We present real-time monitoring of multiple biomolecular interactions by means of high refractive index (HRI) coated long period grating (LPG) working in transition region. The coating was deposited by dip-coating as a thin layer of few hundreds nanometers of atactic polystyrene (PS). The HRI coating was used to enhance the LPG sensitivity to refractive index changes of the surrounding medium and its thickness was determined in order to tune the coated device at the desired working point. To allow immobilization of specific biomolecules, the PS overlay surface was functionalized through bovine serum albumin (BSA) and glutaraldehyde. In particular, BSA was directly adsorbed on PS through strong hydrophobic interactions, then glutaraldehyde was linked atop exploiting the lysines side chains. This intermediate layer allowed to covalently immobilize human IgG (antibody) on the device surface. To prove the immobilization method, the interaction between IgG and its proper anti-human IgG (antigen) was studied. The four binding interactions were on-line monitored following the shift of the LPG attenuation band. The experiment also suggests a novel and interesting biofunctionalization approach of unreactive synthetic polymers with applications in immunosensing.
Detection and Quantitation of Circulating Tumor Cell Dynamics by Bioluminescence Imaging in an Orthotopic Mammary Carcinoma Model (2014)

Circulating tumor cells (CTCs) have been detected in the bloodstream of both early-stage and advanced cancer patients. However, very little is know about the dynamics of CTCs during cancer progression and the clinical relevance of longitudinal CTC enumeration. To address this, we developed a simple bioluminescence imaging assay to detect CTCs in mouse models of metastasis. In a 4T1 orthotopic metastatic mammary carcinoma mouse model, we demonstrated that this quantitative method offers sensitivity down to 2 CTCs in 0.1-1mL blood samples and high specificity for CTCs originating from the primary tumor, independently of their epithelial status. In this model, we simultaneously monitored blood CTC dynamics, primary tumor growth, and lung metastasis progression over the course of 24 days. Early in tumor development, we observed low numbers of CTCs in blood samples (10-15 cells/100 µL) and demonstrated that CTC dynamics correlate with viable primary tumor growth. To our knowledge, these data represent the first reported use of bioluminescence imaging to detect CTCs and quantify their dynamics in any cancer mouse model. This new assay is opening the door to the study of CTC dynamics in a variety of animal models. These studies may inform clinical decision on the appropriate timing of blood sampling and value of longitudinal CTC enumeration in cancer patients.
<title>Single molecule detection in single living cells</title> (2000)

The ability to detect a single analyte molecule represents the ultimate in sensitivity. Single molecule detection has emerged as a powerful tool to characterize heterogeneous systems, in which traditional bulk sampling methods provide a signal averaged over a large number of analytes. Traditionally, single molecule measurements have required highly controlled experimental conditions using ultrapure solvents to create a minimum level of interference. These constraints have primarily limited this technique to examination of systems in vitro. In this report we present the first instance of real-time single molecule detection in living cells. Our experimental approach allows dynamic monitoring of individual fluorophores in vivo, despite the highly complex cellular environment.
The psychology of the unthinkable: Taboo trade-offs, forbidden base rates, and heretical counterfactuals. (2000)

Five studies explored cognitive, affective, and behavioral responses to proscribed forms of social cognition. Experiments 1 and 2 revealed that people responded to taboo trade-offs that monetized sacred values with moral outrage and cleansing. Experiments 3 and 4 revealed that racial egalitarians were least likely to use, and angriest at those who did use, race-tainted base rates and that egalitarians who inadvertently used such base rates tried to reaffirm their fair-mindedness. Experiment 5 revealed that Christian fundamentalists were most likely to reject heretical counterfactuals that applied everyday causal schemata to Biblical narratives and to engage in moral cleansing after merely contemplating such possibilities. Although the results fit the sacred-value-protection model (SVPM) better than rival formulations, the SVPM must draw on cross-cultural taxonomies of relational schemata to specify normative boundaries on thought.
AAV-GRN partially corrects motor deficits and ALS/FTLD-related pathology in Tmem106bGrn mice (2023)

Loss of function of progranulin (PGRN), encoded by the <i>granulin</i> (<i>GRN</i>) gene, is implicated in several neurodegenerative diseases. Several therapeutics to boost PGRN levels are currently in clinical trials. However, it is difficult to test the efficacy of PGRN-enhancing drugs in mouse models due to the mild phenotypes of <i>Grn</i><sup><i>-/-</i></sup> mice. Recently, mice deficient in both PGRN and TMEM106B were shown to develop severe motor deficits and pathology. Here, we show that intracerebral ventricle injection of PGRN-expressing AAV1/9 viruses partially rescues motor deficits, neuronal loss, glial activation, and lysosomal abnormalities in <i>Tmem106b</i><sup><i>-/-</i></sup><i>Grn</i><sup><i>-/-</i></sup> mice. Widespread expression of PGRN is detected in both the brain and spinal cord for both AAV subtypes. However, AAV9 but not AAV1-mediated expression of PGRN results in high levels of PGRN in the serum. Together, these data support using the <i>Tmem106b</i><sup><i>-/-</i></sup><i>Grn</i><sup><i>-/-</i></sup> mouse strain as a robust mouse model to determine the efficacy of PGRN-elevating therapeutics.
Acetyl Bromide-Alcohols as Convenient Reaction Systems for: a) Removal ofN-tert-Boc,N-Cbz AndN-Ac Protective Groups, b) Esterifications and Transesterifications, c) Debenzylation of Aryl-O-Benzyl Ethers (1999)

Abstract Hydrogen bromide generated in situ by the addition of acetyl bromide to alcohols is a useful reagent for esterifications and transesterifications; N-tert-Boc, N-Cbz, and N-Ac deprotections; and debenzylation reactions.
XRBench: An Extended Reality (XR) Machine Learning Benchmark Suite for the Metaverse (2022)

Real-time multi-task multi-model (MTMM) workloads, a new form of deep learning inference workloads, are emerging for applications areas like extended reality (XR) to support metaverse use cases. These workloads combine user interactivity with computationally complex machine learning (ML) activities. Compared to standard ML applications, these ML workloads present unique difficulties and constraints. Real-time MTMM workloads impose heterogeneity and concurrency requirements on future ML systems and devices, necessitating the development of new capabilities. This paper begins with a discussion of the various characteristics of these real-time MTMM ML workloads and presents an ontology for evaluating the performance of future ML hardware for XR systems. Next, we present XRBENCH, a collection of MTMM ML tasks, models, and usage scenarios that execute these models in three representative ways: cascaded, concurrent, and cascaded-concurrent for XR use cases. Finally, we emphasize the need for new metrics that capture the requirements properly. We hope that our work will stimulate research and lead to the development of a new generation of ML systems for XR use cases. XRBench is available as an open-source project: https://github.com/XRBench
Applying Slope Constrained Q-type Aspheres to Reduce Sensitivity of Optical Systems (2012)

Q-type aspheric surfaces that are optimized with slope constraints are not only more testable but also more manufacturable. A lithographic objective and a cell phone camera lens serve as examples to demonstrate this.
Geiger-Mode LiDAR: From Airborne Platforms To Driverless Cars (2017)

The operation of avalanche photodiodes in Geiger mode provides single-photon detection with excellent timing accuracy on a scalable semiconductor device platform. The use of arrays of Geiger-mode detectors for light detection and ranging (LiDAR) from airborne platforms enables the high-rate collection of 3D point cloud imagery from extremely long (&gt;10 km) standoff distances and has resulted in order-of-magnitude increases in performance metrics such as area coverage rate and 3D image resolution. More recently, we have applied Geiger-mode technology to shorter range low-cost LiDAR systems designed for automotive applications. The combination of two factors—single-photon sensitivity and the greater eye-safety of lasers at wavelengths beyond 1400 nm—provides disruptive automotive LiDAR performance that will be essential to future autonomous vehicle navigation.
Reflections on Integrins—Past, Present, and Future (2022)

This Viewpoint discusses the rapid advances in molecular cell biological approaches over the past 50 years and the many avenues for future advances that have been opened, including direct applications for therapeutic and regenerative medicine.
Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland (2021)

The genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75% of these variants in known ID genes were de novo or suspected de novo (64% autosomal dominant; 11% X-linked) and 25% were inherited (14% autosomal recessive; 7% X-linked; and 4% autosomal dominant). A dual molecular diagnosis was suggested in two families (5%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7 Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case.
The Application of Molecular Recognition Technology (MRT) in the Nuclear Power Cycle: From Uranium Mining and Refining to Power Plant Waste Separation and Recovery, as well as Element Analysis and Isotope Purification - 9075 (2009)

This paper reviews the application of Molecular Recognition Technology (MRT) separations technology as an alternative to existing uranium extraction and recovery technologies used in the uranium mining and refining industries. Extraction of deleterious elements from acid mine drainage and aqueous neutral and near neutral mine streams is also discussed as well as applications for MRT in the separation, extraction, recovery and analysis of target elements and ions in power plant and other waste streams and the purification of isotopes such as Pd-103 for brachytherapy.
Nonorthogonal pulseshapes for multicarrier communications in doubly dispersive channels (1998)

A new approach to multicarrier digital communication over time-varying, frequency selective fading channels is presented. We propose a transmission signal set whose basic structure is similar to standard orthogonal frequency division multiple access (OFDM)-setups, i.e., a system of functions generated by time and frequency-shifted versions of a pulse-like prototype function known as a Weyl-Heisenberg (WH) system. Unlike previous OFDM studies, however, which are restricted to the case of orthonormal pulses, we consider nonorthogonal pulses that are adapted to realistically available a priori knowledge of the channel. Perfect transmultiplexing in the case of an ideal channel is incorporated as a mathematical side-constraint. We derive the expected intersymbol/interchannel interference of such a nonorthogonal FDM (NOFDM) system under the assumption of a wide-sense stationary uncorrelated scattering (WSSUS) channel. Based on this result, we compare OFDM and NOFDM schemes with regard to robustness against delay/Doppler spread.
ASM Journals Eliminate Impact Factor Information from Journal Websites (2016)

Many scientists attempt to publish their work in a journal with the highest possible journal impact factor (IF). Despite widespread condemnation of the use of journal IFs to assess the significance of published work, these numbers continue to be widely misused in publication, hiring, funding, and promotion decisions (1, 2).