bluuebunny/crossref_metadata_2025 huggingface dataset:
Schedulability of probabilistic mixed-criticality systems
Authors: Draskovic Stefan , Ahmed Rehan , Huang Pengcheng , Thiele Lothar
Published: February 2021

Mixed-criticality systems often need to fulfill safety standards that dictate different requirements for each criticality level, for example given in the ‘probability of failure per hour’ format. A recent trend suggests designing this kind of systems by jointly scheduling tasks of different criticality levels on a shared platform. When this is done, the usual assumption is that tasks of lower criticality are degraded when a higher criticality task needs more resources, for example when it overruns a bound on its execution time. However, a way to quantify the impact this degradation has on the overall system is not well understood. Meanwhile, to improve schedulability and to avoid over-provisioning of resources due to overly pessimistic worst-case execution time estimates of higher criticality tasks, a new paradigm emerged where task’s execution times are modeled with random variables. In this paper, we analyze a system with probabilistic execution times, and propose metrics that are inspired by safety standards. Among these metrics are the probability of deadline miss per hour, the expected time before degradation happens, and the duration of the degradation. We argue that these quantities provide a holistic view of the system’s operation and schedulability.
PHD Finger Protein 19 Promotes Cardiac Hypertrophy via Epigenetically Regulating SIRT2
Authors: Gu Wei , Cheng Yutong , Wang Su , Sun Tao , Li Zhizhong
Published: February 2021

Epigenetic regulations essentially participate in the development of cardiomyocyte hypertrophy. PHD finger protein 19 (PHF19) is a polycomb protein that controls H3K36me3 and H3K27me3. However, the roles of PHF19 in cardiac hypertrophy remain unknown. Here in this work, we observed that PHF19 promoted cardiac hypertrophy via epigenetically targeting SIRT2. In angiotensin II (Ang II)-induced cardiomyocyte hypertrophy, adenovirus-mediated knockdown ofPhf19reduced the increase in cardiomyocyte size, repressed the expression of hypertrophic marker genesAnpandBnp, as well as inhibited protein synthesis. By contrast,Phf19overexpression promoted Ang II-induced cardiomyocyte hypertrophy in vitro. We also knocked downPhf19expression in mouse hearts in vivo. The results demonstrated thatPhf19knockdown reduced Ang II-induced decline in cardiac fraction shortening and ejection fraction.Phf19knockdown also inhibited Ang II-mediated increase in heart weight, reduced cardiomyocyte size, and repressed the expression of hypertrophic marker genes in mouse hearts. Further mechanism studies showed that PHF19 suppressed the expression of SIRT2, which contributed to the function of PHF19 during cardiomyocyte hypertrophy. PHF19 bound the promoter of SIRT2 and regulated the balance between H3K27me3 and H3K36me3 to repress the expression of SIRT2 in vitro and in vivo. In human hypertrophic hearts, the overexpression of PHF19 and downregulation of SIRT2 were observed. Of importance,PHF19expression was positively correlated with hypertrophic marker genesANPandBNPbut negatively correlated withSIRT2in human hypertrophic hearts. Therefore, our findings demonstrated that PHF19 promoted the development of cardiac hypertrophy via epigenetically regulating SIRT2.
Krylov subspace methods for estimating operator-vector multiplications in Hilbert spaces
Authors: Hashimoto Yuka , Nodera Takashi
Published: February 2021

The Krylov subspace method has been investigated and refined for approximating the behaviors of finite or infinite dimensional linear operators. It has been used for approximating eigenvalues, solutions of linear equations, and operator functions acting on vectors. Recently, for time-series data analysis, much attention is being paid to the Krylov subspace method as a viable method for estimating the multiplications of a vector by an unknown linear operator referred to as a transfer operator. In this paper, we investigate a convergence analysis for Krylov subspace methods for estimating operator-vector multiplications.
Theoretical and computational results of a wave equation with variable exponent and time-dependent nonlinear damping
Authors: Mustafa Muhammad I. , Messaoudi Salim A. , Zahri Mostafa
Published: February 2021

We study the following wave equation $$u_{tt}-\Delta u+\alpha (t)\left| u_{t}\right| ^{m(\cdot )-2}u_{t}=0$$

u

tt

-
Δ
u
+
α

(
t
)

u
t

m
(
·
)
-
2

u
t

=
0

with a nonlinear damping having a variable exponent m(x) and a time-dependent coefficient $$\alpha (t)$$

α
(
t
)

. We use the multiplier method to establish energy decay results depending on both m and $$\alpha $$
α
. We also give four numerical tests to illustrate our theoretical results using the conservative Lax–Wendroff method scheme.
Ability self‐concepts and parental support may protect adolescents when they experience low support from their math teachers
Authors: Lee Glona , Simpkins Sandra D.
Published: February 2021

Introduction

Experiencing low support from teachers can be associated with low academic achievement. Nonetheless, individual‐ (i.e., ability self‐concepts) and contextual‐level (i.e., parental support) protective factors may help adolescents to display academic resilience. This study examined whether high school students’ math ability self‐concepts and parental support can mitigate the possible negative association between perceived low math teacher support and their math achievement.

Method

Correlational data were drawn from the High School Longitudinal Study (N = 14,580, Mage = 17.42 in 11th grade, 51% female), a nationally representative study of high school students in the U.S. The measures of protective factors (i.e., math ability self‐concepts and parental support) were obtained from the surveys administered to students and parents in 9th grade. Students’ perceived teacher support and their math achievement score were measured in 11th grade. A series of linear regression analyses were estimated to test our hypotheses.

Results & Conclusions

Perceived low teacher support was negatively associated with adolescents’ math achievement. Adolescents’ math ability self‐concepts were directly and positively associated with their math achievement. The interaction between perceived low teacher support and ability self‐concepts in predicting adolescents’ achievement varied by parental support. The association between perceived low teacher support and adolescents’ math achievement was not statistically significant when adolescents were high on one of the protective factors. That is, high parental support may be protective for adolescents with low math ability self‐concepts. This study highlights the interaction between adolescents’ academic motivation and parental support in demonstrating resilience to perceived low teacher support.
Computational Screening of Phase-Separating Proteins
Authors: Shen Boyan , Chen Zhaoming , Yu Chunyu , Chen Taoyu , Shi Minglei , Li Tingting
Published: February 2021

Phase separation is an important mechanism that mediates the compartmentalization of proteins in cells. Proteins that can undergo phase separation in cells share certain typical sequence features, like intrinsically disordered regions (IDRs) and multiple modular domains. Sequence-based analysis tools are commonly used in the screening of these proteins. However, current phase separation predictors are mostly designed for IDR-containing proteins, thus inevitably overlook the phase-separating proteins with relatively low IDR content. Features other than amino acid sequence could provide crucial information for identifying possible phase-separating proteins: protein–protein interaction (PPI) networks show multivalent interactions that underlie phase separation process; post-translational modifications (PTMs) are crucial in the regulation of phase separation behavior; spherical structures revealed in immunofluorescence (IF)images indicate condensed droplets formed by phase-separating proteins, distinguishing these proteins from non-phase-separating proteins. Here, we summarize the sequence-based tools for predicting phase-separating proteins and highlight the importance of incorporating PPIs, PTMs, and IF images into phase separation prediction in future studies.
Neurological complications in children with infective endocarditis
Authors: AlBassri Tala , Sheikho Maha , Chaikhouni Farah , Al Habshan Fahad , Kabbani Mohamed S.
Published: February 2021

Background and Objective:

Despite improvement in medical management, infective endocarditis (IE) remains a serious disease that may affect children with and without preexisting cardiac conditions with significant morbidity and mortality. Neurological complications of IE represent the worst with guarded prognosis. The aim of this study is to describe the incidence, etiology, characteristics, risk factors, and outcome of children with neurological complications associated with IE.

Material and methods:

A retrospective cohort study was conducted from 2009 to 2019 where all pediatric patients who fulfilled the modified Duke criteria for IE were included. We divided the cases into 2 groups: IE with neurological complications and IE without neurological complications control group. We compared the two groups statistically and analyzed the results.

Results:

We identified 31 (17 male, 14 female) patients with IE. Neurological complications occurred in 7/31 (23%) patients, mainly in the form of a stroke. Gram-positive microbes were the main causative agents for IE (52%) followed by gram-negative (14%), then fungal organisms (3%). Univariate analysis identified the following risk factors for neurological complications: lower body weight, higher C- reactive protein (CRP) level, and left-sided valvular lesions with P values of (0.0003, 0.0001, and 0.04), respectively.

Although mortality was higher in the neurological complications group, it was 43% in comparison to 21% in the control group and it did not reach statistical significance (P = .49). Large vegetation size (more than 10 mm) was seen in 57% of patients with neurological complications as compared to 16% in the control group (P = .052).

Conclusion:

Neurological complications occurred in almost a quarter of children with IE. Possible risk factors include lower body weight, left-sided valvular lesion, and higher levels of inflammatory markers (CRP). Stroke was the most common neurological complication encountered with possible increased risk of mortality.
Genetics and voice production in childhood and adolescence – a review
Authors: Pedersen Mette , Jønsson Anders Overgård , Larsen Christian F.
Published: February 2021

Adolescence is a challenging time of change in voicing, normally and in pathology. An increased focus on voice production in relation to genetics can expand our knowledge of the onset of puberty and voice change. Our aim with this review was to connect research of genetics to voice production in adolescence. We need further understanding of the developmental background of voice in childhood and adolescence, because many genetic multi handicaps include voice production. Genetic development related to voice production was the focus in a search made by the Royal English Society of Medicine, with only a few results. We supplemented with references to genetic studies of adults and animals as well as adjacent areas of voice production. The genetic development of voice production is steered from the hypothala-mus probably related to growth hormone. The genetic voice production in adults form the basis for understanding development. Some research results were found related to the pubertal steps. The findings are important in the future, using advanced voice analysis and artificial intelligence methods in patients with Multi handicaps.
Usability of fluorescence angiography with indocyanine green in the surgical management of penetrating abdominal trauma: A case series
Authors: Osterkamp Jens T.F. , Patel Mohamed Q. , Steyn Elmin , Svendsen Lars-Bo , Forgan Tim , Achiam Michael P.
Published: February 2021

ABSTRACT

Background:

The surgical management of penetrating abdominal trauma can be challenging, and despite improvements in diagnostics and treatment, mortality and morbidity rates remain high. Intraoperative fluorescence angiography with indocyanine green (ICG-FA) is currently implemented in many elective surgical settings. However, there are few data regarding the usability of ICG-FA in emergency surgery, and to our knowledge, ICG-FA has not been evaluated in penetrating abdominal trauma. Hence, our objective was to determine the feasibility and usability of ICG-FA in surgical management of penetrating abdominal trauma.

Materials and methods:

A total of 20 patients undergoing emergency laparotomy for penetrating abdominal trauma were included. The usability of ICG-FA was evaluated using the System Usability Scale (SUS®). The intraoperative macroscopic assessment was compared with that using ICG-FA, and any influence of ICG-FA on surgical management was documented.

Results:

The ICG-FA was completed in all cases and rendered a “good” median SUS® score of 68.8 (interquartile range, 60.6–82.5) by first-time users. The use of ICG-FA influenced surgical management in 14 cases (70%). In six of those cases, ICG-FA significantly changed surgical management. There were no postoperative complications related to surgical management.

Conclusion:

ICG-FA proved useable and relevant in the setting of penetrating abdominal trauma. Although this was only a small case series, the study showed that ICG-FA could substantially influence surgical management of penetrating abdominal trauma, adding considerable patient benefit.

Highlights
Local anesthetic added to spinal anesthesia; does it stabilize stress hormones after inguinal herniorrhaphy? A randomised controlled trial
Authors: Ghafoor Leila , Razavizadeh Mohammad Reza , Hajian Abbas
Published: February 2021

ABSTRACT

Background:

Elective inguinal hernia repair is a common minor surgery. Early postoperative mobilization without inflammatory related complication is desired.

Methods:

In this randomized controlled trial study 48 adult males were enrolled who experienced elective inguinal hernia repair under spinal anesthesia. Subjects were categorized in 2 groups with equal 24 members in each including patients received local anesthetic (2 mg kg−1 of bupivacaine 0.5%) in addition to spinal anesthesia and controlled who had spinal anesthetic with local placebo injection. Plasma cortisol and prolactin concentration were obtained 1 h before and 3 h after operation. To evaluate severity of postoperative pain the visual analogue scale(VAS) was applied. We also measured the total dosage of analgesic requirement among patients.

Results:

Data showed that spinal anesthesia alone was followed by increasing plasma concentration of either cortisol or prolactin postoperatively (P < 0.01). Findings according to investigate severity of pain implied on that local anesthesia could make more postoperative comfort for patients with inguinal herniorrhaphy(P < 0.001). Therefore, analgesic requirement in patients who were equipped by additional local anesthesia also decreased(P < 0.001).

Conclusions:

We concluded that adding local anesthetic to basic spinal anesthesia during inguinal herniorrhaphy could induce to either lower stress hormones plasma concentration or decrease pain and need for analgesic postoperatively.
Efficacy and safety of systematic corticosteroids among severe COVID-19 patients: a systematic review and meta-analysis of randomized controlled trials
Authors: Ma Shaolei , Xu Changsheng , Liu Shijiang , Sun Xiaodi , Li Renqi , Mao Mingjie , Feng Shanwu , Wang Xian
Published: February 2021

The benefits and harms of corticosteroids for patients with severe coronavirus disease 2019 (COVID-19) remain unclear. We systematically searched PubMed, Embase, and Cochrane Central Register of Controlled Trials from December 31, 2019 to October 1, 2020 to identify randomized controlled trials (RCTs) that evaluated corticosteroids in severe COVID-19 patients. The primary outcome was all-cause mortality at the longest follow-up. Secondary outcomes included a composite disease progression (progression to intubation, ventilation, extracorporeal membrane oxygenation, ICU transfer, or death among those not ventilated at enrollment) and incidence of serious adverse events. A random-effects model was applied to calculate risk ratio (RR) with 95% confidence intervals (CIs). We used the Grading of Recommendations Assessment, Development, and Evaluation approach to evaluate the certainty of the evidence. Seven RCTs involving 6250 patients were included, of which the Randomized Evaluation of COVID-19 Therapy (RECOVERY) trial comprised nearly 78% of all included subjects. Results showed that corticosteroids were associated with a decreased all-cause mortality (27.3 vs. 31.1%; RR: 0.85; 95% CI: 0.73–0.99;P = 0.04; low-certainty evidence). Trial sequential analysis suggested that more trials were still required to confirm the results. However, such survival benefit was absent if RECOVERY trial was excluded (RR: 0.83; 95% CI: 0.65–1.06;P = 0.13). Furthermore, corticosteroids decreased the occurrence of composite disease progression (30.6 vs. 33.3%; RR: 0.77; 95% CI: 0.64–0.92;P = 0.005), but not increased the incidence of serious adverse events (3.5 vs. 3.4%; RR: 1.16; 95% CI: 0.39–3.43;P = 0.79).
Gulf of Mexico blue hole harbors high levels of novel microbial lineages
Authors: Patin N V , Dietrich Z A , Stancil A , Quinan M , Beckler J S , Hall E R , Culter J , Smith C G , Taillefert M , Stewart F J
Published: February 2021

Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole’s rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40–75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80–110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.
Reprogramming the tumor metastasis cascade by targeting galectin-driven networks
Authors: Perrotta Ramiro M. , Bach Camila A. , Salatino Mariana , Rabinovich Gabriel A.
Published: February 2021

A sequence of interconnected events known as the metastatic cascade promotes tumor progression by regulating cellular and molecular interactions between tumor, stromal, endothelial, and immune cells both locally and systemically. Recently, a new concept has emerged to better describe this process by defining four attributes that metastatic cells should undergo. Every individual hallmark represents a unique trait of a metastatic cell that impacts directly in the outcome of the metastasis process. These critical features, known as the hallmarks of metastasis, include motility and invasion, modulation of the microenvironment, cell plasticity and colonization. They are hierarchically regulated at different levels by several factors, including galectins, a highly conserved family of β-galactoside-binding proteins abundantly expressed in tumor microenvironments and sites of metastasis. In this review, we discuss the role of galectins in modulating each hallmark of metastasis, highlighting novel therapeutic opportunities for treating the metastatic disease.
NDP-rhamnose biosynthesis and rhamnosyltransferases: building diverse glycoconjugates in nature
Authors: Wagstaff Ben A. , Zorzoli Azul , Dorfmueller Helge C.
Published: February 2021

Rhamnose is an important 6-deoxy sugar present in many natural products, glycoproteins, and structural polysaccharides. Whilst predominantly found as the l-enantiomer, instances of d-rhamnose are also found in nature, particularly in the Pseudomonads bacteria. Interestingly, rhamnose is notably absent from humans and other animals, which poses unique opportunities for drug discovery targeted towards rhamnose utilizing enzymes from pathogenic bacteria. Whilst the biosynthesis of nucleotide-activated rhamnose (NDP-rhamnose) is well studied, the study of rhamnosyltransferases that synthesize rhamnose-containing glycoconjugates is the current focus amongst the scientific community. In this review, we describe where rhamnose has been found in nature, as well as what is known about TDP-β-l-rhamnose, UDP-β-l-rhamnose, and GDP-α-d-rhamnose biosynthesis. We then focus on examples of rhamnosyltransferases that have been characterized using both in vivo and in vitro approaches from plants and bacteria, highlighting enzymes where 3D structures have been obtained. The ongoing study of rhamnose and rhamnosyltransferases, in particular in pathogenic organisms, is important to inform future drug discovery projects and vaccine development.
A conserved, buried cysteine near the P-site is accessible to cysteine modifications and increases ROS stability in the P-type plasma membrane H+-ATPase
Authors: Welle Marcel , Pedersen Jesper T. , Ravnsborg Tina , Hayashi Maki , Maaß Sandra , Becher Dörte , Jensen Ole N. , Stöhr Christine , Palmgren Michael
Published: February 2021

Sulfur-containing amino acid residues function in antioxidative responses, which can be induced by the reactive oxygen species generated by excessive copper and hydrogen peroxide. In all Na+/K+, Ca2+, and H+ pumping P-type ATPases, a cysteine residue is present two residues upstream of the essential aspartate residue, which is obligatorily phosphorylated in each catalytic cycle. Despite its conservation, the function of this cysteine residue was hitherto unknown. In this study, we analyzed the function of the corresponding cysteine residue (Cys-327) in the autoinhibited plasma membrane H+-ATPase isoform 2 (AHA2) from Arabidopsis thaliana by mutagenesis and heterologous expression in a yeast host. Enzyme kinetics of alanine, serine, and leucine substitutions were identical with those of the wild-type pump but the sensitivity of the mutant pumps was increased towards copper and hydrogen peroxide. Peptide identification and sequencing by mass spectrometry demonstrated that Cys-327 was prone to oxidation. These data suggest that Cys-327 functions as a protective residue in the plasma membrane H+-ATPase, and possibly in other P-type ATPases as well.
CHCHD4 (MIA40) and the mitochondrial disulfide relay system
Authors: Al-Habib Hasan , Ashcroft Margaret
Published: February 2021

Mitochondria are pivotal for normal cellular physiology, as they perform a crucial role in diverse cellular functions and processes, including respiration and the regulation of bioenergetic and biosynthetic pathways, as well as regulating cellular signalling and transcriptional networks. In this way, mitochondria are central to the cell's homeostatic machinery, and as such mitochondrial dysfunction underlies the pathology of a diverse range of diseases including mitochondrial disease and cancer. Mitochondrial import pathways and targeting mechanisms provide the means to transport into mitochondria the hundreds of nuclear-encoded mitochondrial proteins that are critical for the organelle's many functions. One such import pathway is the highly evolutionarily conserved disulfide relay system (DRS) within the mitochondrial intermembrane space (IMS), whereby proteins undergo a form of oxidation-dependent protein import. A central component of the DRS is the oxidoreductase coiled-coil-helix-coiled-coil-helix (CHCH) domain-containing protein 4 (CHCHD4, also known as MIA40), the human homologue of yeast Mia40. Here, we summarise the recent advances made to our understanding of the role of CHCHD4 and the DRS in physiology and disease, with a specific focus on the emerging importance of CHCHD4 in regulating the cellular response to low oxygen (hypoxia) and metabolism in cancer.
HTR6 and SSTR3 targeting to primary cilia
Authors: Barbeito Pablo , Garcia-Gonzalo Francesc R.
Published: February 2021

Primary cilia are hair-like projections of the cell membrane supported by an inner microtubule scaffold, the axoneme, which polymerizes out of a membrane-docked centriole at the ciliary base. By working as specialized signaling compartments, primary cilia provide an optimal environment for many G protein-coupled receptors (GPCRs) and their effectors to efficiently transmit their signals to the rest of the cell. For this to occur, however, all necessary receptors and signal transducers must first accumulate at the ciliary membrane. Serotonin receptor 6 (HTR6) and Somatostatin receptor 3 (SSTR3) are two GPCRs whose signaling in brain neuronal cilia affects cognition and is implicated in psychiatric, neurodegenerative, and oncologic diseases. Over a decade ago, the third intracellular loops (IC3s) of HTR6 and SSTR3 were shown to contain ciliary localization sequences (CLSs) that, when grafted onto non-ciliary GPCRs, could drive their ciliary accumulation. Nevertheless, these CLSs were dispensable for ciliary targeting of HTR6 and SSTR3, suggesting the presence of additional CLSs, which we have recently identified in their C-terminal tails. Herein, we review the discovery and mapping of these CLSs, as well as the state of the art regarding how these CLSs may orchestrate ciliary accumulation of these GPCRs by controlling when and where they interact with the ciliary entry and exit machinery via adaptors such as TULP3, RABL2 and the BBSome.
Pushing the super-resolution limit: recent improvements in microscopy below the diffraction limit
Authors: Nieves D. J. , Baker M. A. B.
Published: February 2021

Super-resolution microscopy has revolutionised the way we observe biological systems. These methods are now a staple of fluorescence microscopy. Researchers have used super-resolution methods in myriad systems to extract nanoscale spatial information on multiple interacting parts. These methods are continually being extended and reimagined to further push their resolving power and achieve truly single protein resolution. Here, we explore the most recent advances at the frontier of the ‘super-resolution’ limit and what opportunities remain for further improvements in the near future.
Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins
Authors: Sanders Joshua C. , Holmstrom Erik D.
Published: February 2021

The conformations of biological macromolecules are intimately related to their cellular functions. Conveniently, the well-characterized dipole–dipole distance-dependence of Förster resonance energy transfer (FRET) makes it possible to measure and monitor the nanoscale spatial dimensions of these conformations using fluorescence spectroscopy. For this reason, FRET is often used in conjunction with single-molecule detection to study a wide range of conformationally dynamic biochemical processes. Written for those not yet familiar with the subject, this review aims to introduce biochemists to the methodology associated with single-molecule FRET, with a particular emphasis on how it can be combined with biomolecular simulations to study diverse interactions between nucleic acids and proteins. In the first section, we highlight several conceptual and practical considerations related to this integrative approach. In the second section, we review a few recent research efforts wherein various combinations of single-molecule FRET and biomolecular simulations were used to study the structural and dynamic properties of biochemical systems involving different types of nucleic acids (e.g., DNA and RNA) and proteins (e.g., folded and disordered).
Applications of atomic force microscopy in modern biology
Authors: Nandi Tathagata , Ainavarapu Sri Rama Koti
Published: February 2021

Single-molecule force spectroscopy (SMFS) is an emerging tool to investigate mechanical properties of biomolecules and their responses to mechanical forces, and one of the most-used techniques for mechanical manipulation is the atomic force microscope (AFM). AFM was invented as an imaging tool which can be used to image biomolecules in sub-molecular resolution in physiological conditions. It can also be used as a molecular force probe for applying mechanical forces on biomolecules. In this brief review, we will provide exciting examples from recent literature which show how the advances in AFM have enabled us to gain deep insights into mechanical properties and mechanobiology of biomolecules. AFM has been applied to study mechanical properties of cells, tissues, microorganisms, viruses as well as biological macromolecules such as proteins. It has found applications in biomedical fields like cancer biology, where it has been used both in the diagnostic phases as well as drug discovery. AFM has been able to answer questions pertaining to mechanosensing by neurons, and mechanical changes in viruses during infection by the viral particles as well as the fundamental processes such as cell division. Fundamental questions related to protein folding have also been answered by SMFS like determination of energy landscape properties of variety of proteins and their correlation with their biological functions. A multipronged approach is needed to diversify the research, as a combination with optical spectroscopy and computer-based steered molecular dynamic simulations along with SMFS can help us gain further insights into the field of biophysics and modern biology.
Reduction of torque and flux ripples in direct torque control for three‐level open‐end winding PMSM drive
Authors: Eshwar Kusuma , Vinay Kumar Thippripati
Published: February 2021

The direct torque control (DTC) of permanent magnet synchronous motor (PMSM) drives is a noticeable practice in industrial applications due to its quick dynamic performance. However, due to the presence of hysteresis controllers and inaccurate switching tables especially for the multilevel fed DTC drives are facing higher ripples in torque and flux response. An improved DTC for three‐level open‐end winding PMSM drive is proposed in this article and features reduction of flux and torque ripples. The torque and flux performances of the PMSM are directly controlled by the calculated reference voltage vector in the stationary reference frame. The voltage vector tables are proposed based on the length of the voltage space vectors and the actual voltage vector nearer to the calculated reference voltage vector is selected so that the minimum ripples exist in flux and torque responses. The steady‐state and dynamic conditions of the proposed DTC method are verified in the real‐time experiment and also compared with the conventional DTC as well as the recently developed control methods.
Digital system for frequency regulation and stabilisation of a four-frequency Zeeman laser gyroscope
Authors: Varenik A.I. , Gorshkov V.N. , Grushin M.E. , Ivanov M.A. , Kolbas Yu.Yu. , Savelyev I.I.
Published: February 2021

We report the results of theoretical and experimental studies of a digital system for regulating and stabilising the frequency of a four-frequency Zeeman laser gyroscope (ZLG), in which generation occurs simultaneously on two longitudinal modes with orthogonal circular polarisations; therefore, four light waves propagate in the optical ring resonator. In contrast to a two-frequency Zeeman laser gyroscope, a four-frequency ZLG does not use the intensity modulation signal of one of the light waves, which appears when an alternating magnetic field is applied to the active medium, to analyse the frequency detuning of longitudinal modes from the centre of the active-medium gain contour. At the same time, it is possible to construct a digital perimeter adjustment system (PAS), which allows the resonator perimeter to be adjusted so that the magnetic components of the zero drift of the gyroscope for two longitudinal generation modes are equal and opposite in sign. Due to this, almost complete compensation for the magnetic component of the zero drift of the gyroscope is realised in a four-frequency ZLG. The use of the digital system makes it possible to provide a higher accuracy of the resonator perimeter adjustment than that in a two-frequency ZLG, even with a relatively small bit capacity of the PAS digital-to-analogue conversion (DAC), and to fully take advantage of the capabilities of a four-frequency ZLG to reduce the magnetic sensitivity.
Optoelectronic reference X-band oscillator for radar systems
Authors: Chizh A.L. , Mikitchuk K.B. , Skotorenko I.V.
Published: February 2021

We present the design and results of studying the characteristics of an optoelectronic microwave oscillator in the free-running regime are presented, propose a method for synchronising it with a signal of a highly stable crystal oscillator using a phase-locked loop, and analyse the results of an experimental study on the frequency instability of an optoelectronic microwave reference oscillator. The optoelectronic microwave reference oscillator with optical gain and a 10 GHz oscillation frequency simultaneously provides ultra-low phase noise (less than – 142 dB Hz−1) at a 10 kHz frequency offset from the microwave carrier and a low level of spurs in the oscillation spectrum (no more than – 94 dBc). In this case, the temperature coefficient of the oscillation frequency is determined by the temperature instability of a highly stable crystal oscillator.
Noise conversion in delay-line optoelectronic microwave oscillators
Authors: Chizh A.L. , Mikitchuk K.B.
Published: February 2021

We report the results of theoretical and experimental studies of noise in a delay-line optoelectronic microwave oscillator with optical gain. The effect of various noise sources on the parameters of an optoelectronic microwave oscillator is considered, and, in addition to the noise of its individual components, several linear and nonlinear mechanisms for converting optical carrier noise into microwave signal noise are taken into account. It is shown that, due to the nonlinearity of the energy characteristics of high-power microwave photodiodes in an optoelectronic generator, the low-frequency components of the laser relative intensity noise are converted into microwave signal noise, as a result of which sources of correlated amplitude and phase noise appear in the oscillator loop.
Spontaneous and stimulated emission of thin-film polymer structures in the presence of nitrotoluene vapour
Authors: Berdybaeva Sh.T. , Tel’minov E.N. , Solodova T.A. , Nikonova E.N. , Samsonova L.G. , Kopylova T.N.
Published: February 2021

The features of spontaneous and stimulated emission of polyfluorenes, polyvinylcarbazole, and low-molecular-weight electron-donor compounds incorporated into various materials are studied in the presence of nitrotoluene vapour. Lasing in planar thin-film waveguides is achieved. The dynamics of the lasing spectra of a thin-film optical chemical sensor is presented. It is shown that the response time of the sensor in the lasing regime is 30 s before the lasing intensity decreases by 50% from the initial level.
Nonlinear optical absorption in thin halide perovskite films under femtosecond excitation at wavelengths of 1064 and 532 nm
Authors: Khudyakov D.V. , Ganin D.V. , Lyashedko A.D. , Frolova L.A. , Troshin P.A. , Lobach A.S.
Published: February 2021

The nonlinear optical responses of perovskite films CsPbI2Br, MAPbI3 + 1% PVC, MA0.15FA0.75Cs0.1PbI2.85Br0.15, and MA0.15FA0.75Cs0.1PbI3, irradiated by femtosecond laser pulses with wavelengths of 1064 and 532 nm, are investigated using z-scan measurements. Nonlinear absorption is found to occur in perovskite films irradiated at a wavelength of 1064 nm; the nonlinear absorption coefficient in thin films (45 – 65 nm) greatly exceeds that in thick ones (120 – 350 nm): 524 – 928 and 38 – 50 cm GW−1, respectively. It is shown that the nonlinear absorption saturation intensity for perovskite films depends on the pump pulse duration and increases with pulse shortening. It is also established that the nonlinear absorption coefficient of organometallic perovskite films exceeds that of a film of inorganic perovskite CsPbI2Br. Bleaching of film samples during z-scanning at a wavelength of 532 nm is related to the irreversible photochemical degradation of films exposed to intense light. The kinetics of photochemical bleaching of the films is detected at a wavelength of 532 nm.
Simulation of a two-dimensional laser diode array directly cooled by coolant flow
Authors: Oleshchenko V.A. , Bogatov A.P. , D’yachkov N.V. , Bezotosnyi V.V.
Published: February 2021

We report an analysis of attained output powers of laser diode bars (LDBs) and power densities of two-dimensional laser diode arrays (LDAs). A new LDA design is proposed and its thermal regime is simulated. The cw output power of the proposed LDA consisting of standard cw LDBs (output power 100 W, efficiency 50%, cavity length 2 mm) can reach 5 kW cm−2. The parameters of a coolant flow in the microchannels of the LDA heat sink necessary to achieve such powers are calculated.
SRS of ultrashort laser pulses with nonlinear phase modulation
Authors: Konyashchenko A.V. , Losev L.L. , Pazyuk V.S.
Published: February 2021

The SRS process in the regime of nonlinear phase modulation of laser and Stokes radiation waves is studied experimentally. The effect of the relationship between the laser and Stokes wavelengths on the value of the minimum laser pulse duration, at which an efficient SRS process is possible, is ascertained. The possibility of obtaining maximally broadband Stokes radiation pulses by matching the group velocities of the laser and Stokes pulses is demonstrated.
Pluripotency state regulates cytoneme selectivity and self-organization of embryonic stem cells
Authors: Junyent Sergi , Reeves Joshua , Gentleman Eileen , Habib Shukry J.
Published: February 2021

To coordinate cell fate with changes in spatial organization, stem cells (SCs) require specific and adaptable systems of signal exchange and cell-to-cell communication. Pluripotent embryonic stem cells (ESCs) use cytonemes to pair with trophoblast stem cells (TSCs) and form synthetic embryonic structures in a Wnt-dependent manner. How these interactions vary with pluripotency states remains elusive. Here we show that ESC transition to an early primed ESC (pESC) state reduces their pairing with TSCs and impairs synthetic embryogenesis. pESCs can activate the Wnt/β-catenin pathway in response to soluble Wnt ligands, but their cytonemes form unspecific and unstable interactions with localized Wnt sources. This is due to an impaired crosstalk between Wnt and glutamate receptor activity and reduced generation of Ca2+ transients on the cytonemes upon Wnt source contact. Induced iGluR activation can partially restore cytoneme function in pESCs, while transient overexpression of E-cadherin improves pESC–TSC pairing. Our results illustrate how changes in pluripotency state alter the mechanisms SCs use to self-organize.
Mechanisms of nonvesicular lipid transport
Authors: Reinisch Karin M. , Prinz William A.
Published: February 2021

We have long known that lipids traffic between cellular membranes via vesicles but have only recently appreciated the role of nonvesicular lipid transport. Nonvesicular transport can be high volume, supporting biogenesis of rapidly expanding membranes, or more targeted and precise, allowing cells to rapidly alter levels of specific lipids in membranes. Most such transport probably occurs at membrane contact sites, where organelles are closely apposed, and requires lipid transport proteins (LTPs), which solubilize lipids to shield them from the aqueous phase during their transport between membranes. Some LTPs are cup like and shuttle lipid monomers between membranes. Others form conduits allowing lipid flow between membranes. This review describes what we know about nonvesicular lipid transfer mechanisms while also identifying many remaining unknowns: How do LTPs facilitate lipid movement from and into membranes, do LTPs require accessory proteins for efficient transfer in vivo, and how is directionality of transport determined?
The actin-regulatory protein Hem-1 is essential for alveolar macrophage development
Authors: Suwankitwat Nutthakarn , Libby Stephen , Liggitt H. Denny , Avalos Alan , Ruddell Alanna , Rosch Jason W. , Park Heon , Iritani Brian M.
Published: February 2021

Hematopoietic protein-1 (Hem-1) is a hematopoietic cell–specific actin-regulatory protein. Loss-of-function (LOF) variants in the NCKAP1L gene encoding Hem-1 have recently been found to result in primary immunodeficiency disease (PID) in humans, characterized by recurring respiratory infections, asthma, and high mortality. However, the mechanisms of how Hem-1 variants result in PID are not known. In this study, we generated constitutive and myeloid cell–specific Nckap1l-KO mice to dissect the importance of Hem-1 in lung immunity. We found that Hem-1–deficient mice accumulated excessive surfactant and cell debris in airways (pulmonary alveolar proteinosis) due to impaired development of alveolar macrophages (AMs) and reduced expression of the AM differentiation factor Pparg. Residual Hem-1–deficient AMs shifted to a proinflammatory phenotype, and Hem-1–deficient neutrophils and monocytes failed to migrate normally. Myeloid cell–specific Hem-1–deficient mice exhibited increased morbidity following influenza A virus or Streptococcus pneumoniae challenge. These results provide potential mechanisms for how LOF variants in Hem-1 result in recurring respiratory diseases.
A high-throughput fluorescence lifetime-based assay to detect binding of myosin-binding protein C to F-actin
Authors: Bunch Thomas A. , Lepak Victoria C. , Bortz Kellan M. , Colson Brett A.
Published: February 2021

Binding properties of actin-binding proteins are typically evaluated by cosedimentation assays. However, this method is time-consuming, involves multiple steps, and has a limited throughput. These shortcomings preclude its use in screening for drugs that modulate actin-binding proteins relevant to human disease. To develop a simple, quantitative, and scalable F-actin–binding assay, we attached fluorescent probes to actin's Cys-374 and assessed changes in fluorescence lifetime upon binding to the N-terminal region (domains C0–C2) of human cardiac myosin-binding protein C (cMyBP-C). The lifetime of all five probes tested decreased upon incubation with cMyBP-C C0–C2, as measured by time-resolved fluorescence (TR-F), with IAEDANS being the most sensitive probe that yielded the smallest errors. The TR-F assay was compared with cosedimentation to evaluate in vitro changes in binding to actin and actin–tropomyosin arising from cMyBP-C mutations associated with hypertrophic cardiomyopathy (HCM) and tropomyosin binding. Lifetime changes of labeled actin with added C0–C2 were consistent with cosedimentation results. The HCM mutation L352P was confirmed to enhance actin binding, whereas PKA phosphorylation reduced binding. The HCM mutation R282W, predicted to disrupt a PKA recognition sequence, led to deficits in C0–C2 phosphorylation and altered binding. Lastly, C0–C2 binding was found to be enhanced by tropomyosin and binding capacity to be altered by mutations in a tropomyosin-binding region. These findings suggest that the TR-F assay is suitable for rapidly and accurately determining quantitative binding and for screening physiological conditions and compounds that affect cMyBP-C binding to F-actin for therapeutic discovery.
Phosphate has dual roles in cross-bridge kinetics in rabbit psoas single myofibrils
Authors: Kawai Masataka , Stehle Robert , Pfitzer Gabriele , Iorga Bogdan
Published: February 2021

In this study, we aimed to study the role of inorganic phosphate (Pi) in the production of oscillatory work and cross-bridge (CB) kinetics of striated muscle. We applied small-amplitude sinusoidal length oscillations to rabbit psoas single myofibrils and muscle fibers, and the resulting force responses were analyzed during maximal Ca2+ activation (pCa 4.65) at 15°C. Three exponential processes, A, B, and C, were identified from the tension transients, which were studied as functions of Pi concentration ([Pi]). In myofibrils, we found that process C, corresponding to phase 2 of step analysis during isometric contraction, is almost a perfect single exponential function compared with skinned fibers, which exhibit distributed rate constants, as described previously. The [Pi] dependence of the apparent rate constants 2πb and 2πc, and that of isometric tension, was studied to characterize the force generation and Pi release steps in the CB cycle, as well as the inhibitory effect of Pi. In contrast to skinned fibers, Pi does not accumulate in the core of myofibrils, allowing sinusoidal analysis to be performed nearly at [Pi] = 0. Process B disappeared as [Pi] approached 0 mM in myofibrils, indicating the significance of the role of Pi rebinding to CBs in the production of oscillatory work (process B). Our results also suggest that Pi competitively inhibits ATP binding to CBs, with an inhibitory dissociation constant of ∼2.6 mM. Finally, we found that the sinusoidal waveform of tension is mostly distorted by second harmonics and that this distortion is closely correlated with production of oscillatory work, indicating that the mechanism of generating force is intrinsically nonlinear. A nonlinear force generation mechanism suggests that the length-dependent intrinsic rate constant is asymmetric upon stretch and release and that there may be a ratchet mechanism involved in the CB cycle.