A semi-empirical approach to calibrate simulation models for semiconductor devices.

Semiconductor device optimization using computer-based prototyping techniques like simulation or machine learning digital twins can be time and resource efficient compared to the conventional strategy of iterating over device design variations by fabricating the actual device. Ideally, simulation models require perfect calibration of material parameters for the model to represent a particular semiconductor device. This calibration process itself can require characterization information of the device and its precursors and extensive expert knowledge of non characterizable parameters and their tuning. We propose a hybrid method to calibrate multiple simulation models for a device using minimal characterization data and machine learning-based prediction models. A photovoltaic device is chosen as the example for this technique where optical and electrical simulation models of an industrially manufactured silicon solar cell are calibrated and the simulated device performance is compared with the measurement data from the physical device.

Aurintricarboxylic acid protects isoproterenol induced left ventricular hypertrophy by modulating TWEAK signaling.

BACKGROUND: Cardiac hypertrophy is regarded as a compensation mechanism to overcome the increased workload. Aurintricarboxylic acid (ATA) is a derivative of quinomethanes and a selective inhibitor of TWEAK/Fn14 pathway. In this study, we investigated the effect of ATA on isoproterenol (ISO)-induced pathological cardiac hypertrophy. METHODS: Cardiac hypertrophy in H9C2 cells was induced using ISO 20 µM dissolved in PBS. H9C2 cells were treated with ATA (5 µM, 10 µM, 20 µM) followed by ISO stimulation for 24 h. Male SD rats were injected ISO (5 mg/kg/day, s.c) for 21 days and followed by treatment with ATA (10 mg/kg, i.p.) for 14 days. Cardiac functions were assessed. After sacrifice, hearts were subjected to histopathological and western blot analysis. RESULTS: In in-vitro results, upon ATA treatment, ICC results showed significant decrease in TWEAK and ANP expression. In in-vivo results, echocardiography showed significant restoration of cardiac function in ATA treated rats. Histopathological analysis showed a significant decrease in left ventricular wall thickness, cardiomyocytes width and reduced fibrosis in ATA treated rats. Western blotting showed decreased expression of the cardiac hypertrophy maker ANP, inflammatory markers including TWEAK and apoptotic markers after ATA treatment. CONCLUSION: These findings suggested that the TWEAK/Fn14 pathway could be a potential target for therapeutic exploration in ISO induced cardiac hypertrophy. ATA, as an inhibitor of this pathway, exerted significant cardioprotective effect against ISO-induced cardiac hypertrophy in rats.

Label-free protocol to quantify protein affinity using isothermal titration calorimetry and bio-layer interferometry of a human eIF5-mimic protein.

eIF5-mimic protein (5MP) controls translation through its interaction with eukaryotic translation initiation factor (eIF) 2 and eIF3 and alters non-AUG translation rates for oncogenes in cancer and repeat expansions in neurodegenerative disease. To precisely evaluate the effect of 5MP mutations on binding affinity against eIFs, here we describe two label-free protocols of affinity measurement for 5MP binding to eIF2 or eIF3 protein segments, termed isothermal titration calorimetry (ITC) and bio-layer interferometry (BLI), starting with how to purify proteins used. For complete details on the use and execution of this protocol, please refer to Singh et al. (2021).

Lightweight deep convolutional neural network for background sound classification in speech signals.

Recognizing background information in human speech signals is a task that is extremely useful in a wide range of practical applications, and many articles on background sound classification have been published. It has not, however, been addressed with background embedded in real-world human speech signals. Thus, this work proposes a lightweight deep convolutional neural network (CNN) in conjunction with spectrograms for an efficient background sound classification with practical human speech signals. The proposed model classifies 11 different background sounds such as airplane, airport, babble, car, drone, exhibition, helicopter, restaurant, station, street, and train sounds embedded in human speech signals. The proposed deep CNN model consists of four convolution layers, four max-pooling layers, and one fully connected layer. The model is tested on human speech signals with varying signal-to-noise ratios (SNRs). Based on the results, the proposed deep CNN model utilizing spectrograms achieves an overall background sound classification accuracy of 95.2% using the human speech signals with a wide range of SNRs. It is also observed that the proposed model outperforms the benchmark models in terms of both accuracy and inference time when evaluated on edge computing devices.

Human oncoprotein 5MP suppresses general and repeat-associated non-AUG translation via eIF3 by a common mechanism.

eIF5-mimic protein (5MP) is a translational regulatory protein that binds the small ribosomal subunit and modulates its activity. 5MP is proposed to reprogram non-AUG translation rates for oncogenes in cancer, but its role in controlling non-AUG initiated synthesis of deleterious repeat-peptide products, such as FMRpolyG observed in fragile-X-associated tremor ataxia syndrome (FXTAS), is unknown. Here, we show that 5MP can suppress both general and repeat-associated non-AUG (RAN) translation by a common mechanism in a manner dependent on its interaction with eIF3. Essentially, 5MP displaces eIF5 through the eIF3c subunit within the preinitiation complex (PIC), thereby increasing the accuracy of initiation. In Drosophila, 5MP/Kra represses neuronal toxicity and enhances the lifespan in an FXTAS disease model. These results implicate 5MP in protecting cells from unwanted byproducts of non-AUG translation in neurodegeneration.

Towards Development of a Non-Intrusive and Label-Free THz Sensor for Rapid Detection of Aqueous Bio-Samples Using Microfluidic Approach.

As most of the bio-molecules sizes are comparable to the terahertz (THz) wavelength, this frequency range has spurred great attention for bio-medical and bio-sensing applications. Utilizing such capabilities of THz electromagnetic wave, this paper presents the design and analysis of a new non-intrusive and label-free THz bio-sensor for aqueous bio-samples using the microfluidic approach with real-time monitoring. The proposed THz sensor unit utilizes the highly confined feature of the localized spoof surface plasmon (LSSP) resonator to get high sensitivity for any minute change in the dielectric value near it's surface. The proposed sensor, which is designed at 1 THz, exploits the reflection behavior (S11) of the LSSP resonator as the sensing response. The proposed sensor has been designed with a high-quality factor of 192 to obtain a high sensitivity of 13.5 MHz/mgml-1. To validate the proposed concept, a similar sensor unit has been designed and implemented at microwave frequency owing to the geometry dependent characteristics of the LSSP. The developed sensor has got a highly sensitive response at microwave frequency with a sensitivity of 1.2771e-4 MHz/mgml-1. A customized read-out circuitry is also designed and developed to get the sensor response in terms of DC-voltage and to provide a proof of concept for the low-cost point of care (PoC) detection solution using the proposed sensor. It is anticipated that the proposed design of highly sensitive sensor will pave a path to develop lab-on-chip systems for bio-sensing applications.

Non-psychiatric Referral among First Encounter Patients Attending the Psychiatry Out Patient Services of a Tertiary Care Hospital: A Descriptive Cross-sectional Study.

INTRODUCTION: Pathway of psychiatric care is defined as the sequence of contacts with individuals and organizations initiated by the distressed person's efforts and his significant others to seek appropriate health care. This study aimed to find the prevalence of non-psychiatric referral as first encounter among patients attending the psychiatry outpatient department of a tertiary care hospital. METHODS: A descriptive cross-sectional study was carried out from 29th March 2015 to 25th April 2015 in the outpatient department of the department of psychiatry of a tertiary via direct interview using the World Health Organization's encounter form. Ethical approval was taken from undergraduate medical research protocol review board (Reference number 105/071/072). Psychiatric diagnoses were made by respective consultants using the International Classification of Diseases-10 Clinical Descriptions and Diagnostic Guidelines criteria. Data was entered in the Microsoft Excel 2007 and analyzed by Stata version 15. Point estimate at 95% Confidence Interval was calculated along with frequency and percentage for binary data. RESULTS: Out of 50 patients, 26 (52%) (38.2-65.8 at 95% Confidence Interval) of new cases in the outpatient department had non-psychiatric referrals. Among them, 13 (26%) referred from faith healers, 7 (14%) from the general hospital and 6 (12%) from medical out patient department. CONCLUSIONS: The prevalence of non-psychiatric referral for the patients seen for the first time in the psychiatry outpatient department was similar to findings from studies done in different parts of South East Asia.

Bubble CPAP splitting: innovative strategy in resource-limited settings.

BACKGROUND: Non-invasive respiratory support for neonates using bubble continuous positive airway pressure (bCPAP) delivery systems is now widespread owing to its safety, cost effectiveness and easy applicability. Many innovative solutions have been suggested to deal with the possible shortage in desperate situations like disasters, pandemics and resource-limited settings. Although splitting of invasive ventilation has been reported previously, no attempts to split non-invasive respiratory support have been reported. OBJECTIVE: The primary objective was to test the feasibility of splitting the bCPAP assembly using a T-piece splitter in a simulation model. METHODS: A pilot simulation-based study was done to split a single bCPAP assembly using a T-piece. Other materials consisted of a heated humidification system, an air oxygen blender, corrugated inspiratory and expiratory tubing, nasal interfaces and two intercostal chest tube drainage bags. Two pressure manometers were used simultaneously to measure delivered pressures at different levels of set bCPAPs at the expiratory limb of nasal interfaces. RESULTS: Pressures measured at the expiratory end of two nasal interfaces were 5.1 and 5.2 cm H2O, respectively, at a flow of 6 L/min and a water level of 5 cm H2O in both chest bags. When tested across different levels of set continuous positive airway pressure (3-8 cmH2O) and fractional inspired oxygen concentration (0.30-1.0), measured parameters corresponded to set parameters. CONCLUSION: bCPAP splitting using a T-piece splitter is a technically simple, feasible and reliable strategy tested in a simulation model. Further testing is needed in a simulated lung model.

The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states.

The adeno-associated virus (AAV) non-structural Rep proteins catalyze all the DNA transactions required for virus viability including, DNA replication, transcription regulation, genome packaging, and during the latent phase, site-specific integration. Rep proteins contain two multifunctional domains: an Origin Binding Domain (OBD) and a SF3 helicase domain (HD). Studies have shown that Rep proteins have a dynamic oligomeric behavior where the nature of the DNA substrate molecule modulates its oligomeric state. In the presence of ssDNA, Rep68 forms a large double-octameric ring complex. To understand the mechanisms underlying AAV Rep function, we investigated the cryo-EM and X-ray structures of Rep68-ssDNA complexes. Surprisingly, Rep68 generates hybrid ring structures where the OBD forms octameric rings while the HD forms heptamers. Moreover, the binding to ATPγS promotes a large conformational change in the entire AAA+ domain that leads the HD to form both heptamer and hexamers. The HD oligomerization is driven by an interdomain linker region that acts as a latch to 'catch' the neighboring HD subunit and is flexible enough to permit the formation of different stoichiometric ring structures. Overall, our studies show the structural basis of AAV Rep's structural flexibility required to fulfill its multifunctional role during the AAV life cycle.

The transcription factor NFAT5 limits infection-induced type I interferon responses.

Type I interferon (IFN-I) provides effective antiviral immunity but can exacerbate harmful inflammatory reactions and cause hematopoietic stem cell (HSC) exhaustion; therefore, IFN-I expression must be tightly controlled. While signaling mechanisms that limit IFN-I induction and function have been extensively studied, less is known about transcriptional repressors acting directly on IFN-I regulatory regions. We show that NFAT5, an activator of macrophage pro-inflammatory responses, represses Toll-like receptor 3 and virus-induced expression of IFN-I in macrophages and dendritic cells. Mice lacking NFAT5 exhibit increased IFN-I production and better control of viral burden upon LCMV infection but show exacerbated HSC activation under systemic poly(I:C)-induced inflammation. We identify IFNß as a primary target repressed by NFAT5, which opposes the master IFN-I inducer IRF3 by binding to an evolutionarily conserved sequence in the IFNB1 enhanceosome that overlaps a key IRF site. These findings illustrate how IFN-I responses are balanced by simultaneously opposing transcription factors.

Plasmonic metamaterial-based filtering structures with dynamic tunability.

In this Letter, we report the design, analysis, and characterization of first- and second-order plasmonic metamaterial-based multi-mode filtering structures. Further, electronic adaptivity in filter transfer functions is introduced and characterized. First, the basic operating principle of the engineered multi-mode resonator-based bandpass filter is presented. Then the concept is extended by introducing electronic (dynamic) tuning of the bandwidth using semiconductor varactor diodes. Afterwards, to enhance the selectivity and out-of-band filtering response, second-order multi-mode designs are realized. For experimental verification, the hardware prototype is fabricated and characterized using the Keysight analyzer N9918A. The design filtering structures will pave an important role in tunable plasmonic circuits and systems.

A novel λ integrase-mediated seamless vector transgenesis platform for therapeutic protein expression.

Advances in stem cell engineering, gene therapy and molecular medicine often involve genome engineering at a cellular level. However, functionally large or multi transgene cassette insertion into the human genome still remains a challenge. Current practices such as random transgene integration or targeted endonuclease-based genome editing are suboptimal and might pose safety concerns. Taking this into consideration, we previously developed a transgenesis tool derived from phage λ integrase (Int) that precisely recombines large plasmid DNA into an endogenous sequence found in human Long INterspersed Elements-1 (LINE-1). Despite this advancement, biosafety concerns associated with bacterial components of plasmids, enhanced uptake and efficient transgene expression remained problematic. We therefore further improved and herein report a more superior Int-based transgenesis tool. This novel Int platform allows efficient and easy derivation of sufficient amounts of seamless supercoiled transgene vectors from conventional plasmids via intramolecular recombination as well as subsequent intermolecular site-specific genome integration into LINE-1. Furthermore, we identified certain LINE-1 as preferred insertion sites for Int-mediated seamless vector transgenesis, and showed that targeted anti-CD19 chimeric antigen receptor gene integration achieves high-level sustained transgene expression in human embryonic stem cell clones for potential downstream therapeutic applications.

Functional architecture of the Reb1-Ter complex of Schizosaccharomyces pombe.

Reb1 ofSchizosaccharomyces pomberepresents a family of multifunctional proteins that bind to specific terminator sites (Ter) and cause polar termination of transcription catalyzed by RNA polymerase I (pol I) and arrest of replication forks approaching the Ter sites from the opposite direction. However, it remains to be investigated whether the same mechanism causes arrest of both DNA transactions. Here, we present the structure of Reb1 as a complex with a Ter site at a resolution of 2.7 Å. Structure-guided molecular genetic analyses revealed that it has distinct and well-defined DNA binding and transcription termination (TTD) domains. The region of the protein involved in replication termination is distinct from the TTD. Mechanistically, the data support the conclusion that transcription termination is not caused by just high affinity Reb1-Ter protein-DNA interactions. Rather, protein-protein interactions between the TTD with the Rpa12 subunit of RNA pol I seem to be an integral part of the mechanism. This conclusion is further supported by the observation that double mutations in TTD that abolished its interaction with Rpa12 also greatly reduced transcription termination thereby revealing a conduit for functional communications between RNA pol I and the terminator protein.

Crystallization and preliminary X-ray characterization of the eukaryotic replication terminator Reb1-Ter DNA complex.

The Reb1 protein from Schizosaccharomyces pombe is a member of a family of proteins that control programmed replication termination and/or transcription termination in eukaryotic cells. These events occur at naturally occurring replication fork barriers (RFBs), where Reb1 binds to termination (Ter) DNA sites and coordinates the polar arrest of replication forks and transcription approaching in opposite directions. The Reb1 DNA-binding and replication-termination domain was expressed in Escherichia coli, purified and crystallized in complex with a 26-mer DNA Ter site. Batch crystallization under oil was required to produce crystals of good quality for data collection. Crystals grew in space group P21, with unit-cell parameters a = 68.9, b = 162.9, c = 71.1 Å, ß = 94.7°. The crystals diffracted to a resolution of 3.0 Å. The crystals were mosaic and required two or three cycles of annealing. This study is the first to yield structural information about this important family of proteins and will provide insights into the mechanism of replication and transcription termination.

Cryo-electron microscopic structure of SecA protein bound to the 70S ribosome.

SecA is an ATP-dependent molecular motor pumping secretory and outer membrane proteins across the cytoplasmic membrane in bacteria. SecA associates with the protein-conducting channel, the heterotrimeric SecYEG complex, in a so-called posttranslational manner. A recent study further showed binding of a monomeric state of SecA to the ribosome. However, the true oligomeric state of SecA remains controversial because SecA can also form functional dimers, and high-resolution crystal structures exist for both the monomer and the dimer. Here we present the cryo-electron microscopy structures of Escherichia coli SecA bound to the ribosome. We show that not only a monomeric SecA binds to the ribosome but also that two copies of SecA can be observed that form an elongated dimer. Two copies of SecA completely surround the tunnel exit, providing a unique environment to the nascent polypeptides emerging from the ribosome. We identified the N-terminal helix of SecA required for a stable association with the ribosome. The structures indicate a possible function of the dimeric form of SecA at the ribosome.

Biotin-tagged probes for MMP expression and activation: design, synthesis, and binding properties.

The design and synthesis of biotin chain-terminated inhibitors (BTI) showing high affinity for matrix metalloproteinases (MMPs) on one side and high affinity for avidin through the biotinylated tag on the other are reported. The affinity of the designed BTI toward five different MMPs has been evaluated and the simultaneous formation of a highly stable ternary system Avidin-BTI-MMP clearly assessed. This system will permit the development of new approaches to detect, quantify, or collect MMPs in biological samples, with potential applications in vivo.

Evidence of reciprocal reorientation of the catalytic and hemopexin-like domains of full-length MMP-12.

The proteolytic activity of matrix metalloproteinases toward extracellular matrix components (ECM), cytokines, chemokines, and membrane receptors is crucial for several homeostatic and pathological processes. Active MMPs are a family of single-chain enzymes (23 family members in the human genome), most of which constituted by a catalytic domain and by a hemopexin-like domain connected by a linker. The X-ray structures of MMP-1 and MMP-2 suggest a conserved and well-defined spatial relationship between the two domains. Here we present structural data for MMP-12, suitably stabilized against self-hydrolysis, both in solution (NMR and SAXS) and in the solid state (X-ray), showing that the hemopexin-like and the catalytic domains experience conformational freedom with respect to each other on a time scale shorter than 10(-8) s. Hints on the probable conformations are also obtained. This experimental finding opens new perspectives for the often hypothesized active role of the hemopexin-like domain in the enzymatic activity of MMPs.