bluuebunny/crossref_metadata_2025_split huggingface dataset:
USP52 regulates DNA end resection and chemosensitivity through removing inhibitory ubiquitination from CtIP
Authors: Gao Ming , Guo Guijie , Huang Jinzhou , Kloeber Jake A. , Zhao Fei , Deng Min , Tu Xinyi , Kim Wootae , Zhou Qin , Zhang Chao , Yin Ping , Luo Kuntian , Lou Zhenkun 
Published: October 2020

AbstractHuman C-terminal binding protein (CtBP)–interacting protein (CtIP) is a central regulator to initiate DNA end resection and homologous recombination (HR). Several studies have shown that post-translational modifications control the activity or expression of CtIP. However, it remains unclear whether and how cells restrain CtIP activity in unstressed cells and activate CtIP when needed. Here, we identify that USP52 directly interacts with and deubiquitinates CtIP, thereby promoting DNA end resection and HR. Mechanistically, USP52 removes the ubiquitination of CtIP to facilitate the phosphorylation and activation of CtIP at Thr-847. In addition, USP52 is phosphorylated by ATM at Ser-1003 after DNA damage, which enhances the catalytic activity of USP52. Furthermore, depletion of USP52 sensitizes cells to PARP inhibition in a CtIP-dependent manner in vitro and in vivo. Collectively, our findings reveal the key role of USP52 and the regulatory complexity of CtIP deubiquitination in DNA repair.
Fenton reaction mechanism generating no OH radicals in Nafion membrane decomposition
Authors: Tsuneda Takao 
Published: October 2020

AbstractMechanism of Fenton reaction, which is a most widely-used degradation test for organic materials using hydrogen peroxide (H$$_2$$

2

O$$_2$$

2

) and iron (Fe) cations, is revealed for the decomposition of hydrated Nafion membrane. This reaction mechanism has been assumed to generate OH radicals. For a doubly-hydrated Nafion membrane model, Fenton reaction with divalent and monovalent Fe (Fe$$^{2+}$$

2
+

and Fe$$^+$$

+

) cation hydration complexes is explored for experimentally-supported hydration numbers using long-range correction for density functional theory. As a result, it is found that H$$_2$$

2

O$$_2$$

2

coordinating to the Fe$$^{2+}$$

2
+

hydration complexes first approaches Nafion side chains in high humidity, then leads to the C–S bond dissociation of the side chain to produce carbonic acid group and sulfonic acid ion. On the other hand, once electron transfer proceeds between iron ions, the O–O bond of the coordinating H$$_2$$

2

O$$_2$$

2

is extended, then the C–S bond is dissociated to produce trihydroxymethyl group and sulfur trioxide, which are rapidly transformed to carboxyl group and sulfonic acid ion in aquo. This mechanism is confirmed by the vibrational spectrum analysis of the decomposed product. Collective Nafion decomposition mechanisms also suggest that the decomposition reaction uses the recycle of generated Fe cation hydration complexes under acidic condition near membrane surface.
Neddylation blockade induces HIF-1α driven cancer cell migration via upregulation of ZEB1
Authors: Park Jun Bum , Seo Jieun , Park Jong-Wan , Chun Yang-Sook 
Published: October 2020

AbstractNeddylation is a process by which NEDD8 is covalently conjugated to target proteins by sequential enzymatic reaction. Its role in cancer cell migration has only been recently acknowledged. Previously in cancer cell migration, the epithelial to mesenchymal transition (EMT) process has been well-known to play an important role in both invasion and metastasis by promoting mesenchymal phenotype in epithelial cells. However, the role of neddylation in the EMT process and its mechanistic details are yet to be elucidated. We recently reported that neddylation plays a crucial role in cancer cell migration through the PI3K-Akt pathway. Here, we report that inhibiting neddylation activates the hypoxia-inducible factor 1α (HIF-1α) through the PI3K-Akt pathway, which eventually regulates the EMT-activator ZEB1 (zinc finger E-box binding homeobox 1) in various cancer cell lines. As induction of HIF-1α is known to deteriorate the state of cancer and EMT process is one of the hallmarks of metastasis in cancer, our findings uncover the role of neddylation between HIF-1α and ZEB1.
Prevalence and associated factors of cataract and cataract-related blindness in the Russian Ural Eye and Medical Study
Authors: Bikbov Mukharram M. , Kazakbaeva Gyulli M. , Gilmanshin Timur R. , Zainullin Rinat M. , Nuriev Ildar F. , Zaynetdinov Artur F. , Israfilova Gulnara Z. , Panda-Jonas Songhomitra , Arslangareeva Inga I. , Rakhimova Ellina M. , Rusakova Iulia A. , Jonas Jost B. 
Published: October 2020

AbstractTo assess the prevalence of cataract and cataract surgery in a population from Russia, we conducted the population-based Ural Eye and Medical Study with 5899 participants (80.5% out of 7328 eligible individuals), with an age of 40 + years as the eligibility criterion. In the phakic population, the prevalence of nuclear, cortical, subcapsular cataract and any cataract was 38.0% [95% confidence interval (CI) 36.6, 39.3], 14.5% (95% CI 13.5, 15.5), 0.6% (95% CI 0.4, 0.8) and 44.6% (95% CI 43.2, 46.0), respectively. A higher prevalence of nuclear cataract was associated with older age [odds ratio (OR) 1.10; 95% CI 1.10, 1.11], the female sex (OR 1.27; 95% CI 1.08, 1.50), urban region (OR 2.00; 95% CI 1.71, 2.33), a low educational level (OR 0.93; 95% CI 0.88, 0.98), a high diastolic blood pressure (OR 1.01; 95% CI 1.001, 1.02), a low serum concentration of high-density lipoproteins (OR 0.91; 95% CI 0.84, 0.98), more smoking package years (OR 1.01; 95% CI 1.01, 1.02), chronic kidney disease (OR 1.02; 95% CI 1.10, 1.03), a short axial length (OR 0.93; 95% CI 0.86, 0.99), and a low prevalence of age-related macular degeneration (OR 0.72; 95% CI 0.57, 0.92). The prevalence of previous cataract surgery conducted in 354/5885 individuals (6.0%; 95% CI 5.4, 6.6) increased from 0.4% (95% CI 0.0, 1.0) in the age group of 40–45 years to 37.6% (95% CI 30.9, 44.4) in the age group of 80 + years. Cataract was the cause of moderate-to-severe vision impairment in 109 (1.8%) individuals and of blindness in three (0.05%) individuals. The prevalence of cataract and cataract-related MSVI and blindness were relatively high; subsequently, the prevalence of previous cataract surgery was relatively low in this population from Russia.
RecQ helicases in DNA repair and cancer targets
Authors: Newman Joseph A. , Gileadi Opher 
Published: October 2020

Abstract
Helicases are enzymes that use the energy derived from ATP hydrolysis to catalyze the unwinding of DNA or RNA. The RecQ family of helicases is conserved through evolution from prokaryotes to higher eukaryotes and plays important roles in various DNA repair pathways, contributing to the maintenance of genome integrity. Despite their roles as general tumor suppressors, there is now considerable interest in exploiting RecQ helicases as synthetic lethal targets for the development of new cancer therapeutics. In this review, we summarize the latest developments in the structural and mechanistic study of RecQ helicases and discuss their roles in various DNA repair pathways. Finally, we consider the potential to exploit RecQ helicases as therapeutic targets and review the recent progress towards the development of small molecules targeting RecQ helicases as cancer therapeutics.
Nucleosynthetic yields of Z = 10−5 intermediate-mass stars
Authors: Gil-Pons P. , Doherty C. L. , Gutiérrez J. , Campbell S. W. , Siess L. , Lattanzio J. C. 
Published: October 2020

Context. Observed abundances of extremely metal-poor stars in the Galactic halo hold clues for understanding the ancient universe. Interpreting these clues requires theoretical stellar models in a wide range of masses in the low-metallicity regime. The existing literature is relatively rich with extremely metal-poor massive and low-mass stellar models. However, relatively little information is available on the evolution of intermediate-mass stars of Z ≲ 10−5, and the impact of the uncertain input physics on the evolution and nucleosynthesis has not yet been systematically analysed.
Aims. We aim to provide the nucleosynthetic yields of intermediate-mass Z = 10−5 stars between 3 and 7.5 M⊙, and quantify the effects of the uncertain wind rates. We expect these yields could eventually be used to assess the contribution to the chemical inventory of the early universe, and to help interpret abundances of selected C-enhanced extremely metal-poor (CEMP) stars.
Methods. We compute and analyse the evolution of surface abundances and nucleosynthetic yields of Z = 10−5 intermediate-mass stars from their main sequence up to the late stages of their thermally pulsing (Super) AGB phase, with different prescriptions for stellar winds. We use the postprocessing code MONSOON to compute the nucleosynthesis based on the evolution structure obtained with the Monash-Mount Stromlo stellar evolution code MONSTAR. By comparing our models and others from the literature, we explore evolutionary and nucleosynthetic trends with wind prescriptions and with initial metallicity (in the very low-Z regime). We also compare our nucleosynthetic yields to observations of CEMP-s stars belonging to the Galactic halo.
Results. The yields of intermediate-mass extremely metal-poor stars reflect the effects of very deep or corrosive second dredge-up (for the most massive models), superimposed with the combined signatures of hot-bottom burning and third dredge-up. Specifically, we confirm the reported trend that models with initial metallicity Zini ≲ 10−3 give positive yields of 12C, 15N, 16O, and 26Mg. The 20Ne, 21Ne, and 24Mg yields, which were reported to be negative at Zini ≳ 10−4, become positive for Z = 10−5. The results using two different prescriptions for mass-loss rates differ widely in terms of the duration of the thermally pulsing (Super) AGB phase, overall efficiency of the third dredge-up episode, and nucleosynthetic yields. We find that the most efficient of the standard wind rates frequently used in the literature seems to favour agreement between our yield results and observational data. Regardless of the wind prescription, all our models become N-enhanced EMP stars.
Dust emission, extinction, and scattering in LDN 1642
Authors: Juvela Mika , Neha Sharma , Mannfors Emma , Saajasto Mika , Ysard Nathalie , Pelkonen Veli-Matti 
Published: October 2020

Context. LDN 1642 is a rare example of a star-forming, high-latitude molecular cloud. The dust emission of LDN 1642 has already been studied extensively in the past, but its location also makes it a good target for studies of light scattering.
Aims. We wish to study the near-infrared (NIR) light scattering in LDN 1642, its correlation with the cloud structure, and the ability of dust models to simultaneously explain observations of sub-millimetre dust emission, NIR extinction, and NIR scattering.
Methods. We used observations made with the HAWK-I instrument to measure the NIR surface brightness and extinction in LDN 1642. These data were compared with Herschel observations of dust emission and, with the help of radiative transfer modelling, with the predictions calculated for different dust models.
Results. We find, for LDN 1642, an optical depth ratio τ(250 μm)∕τ(J) ≈ 10−3, confirming earlier findings of enhanced sub-millimetre emissivity. The relationships between the column density derived from dust emission and the NIR colour excesses are linear and consistent with the shape of the standard NIR extinction curve. The extinction peaks at AJ = 2.6 mag, and the NIR surface brightness remains correlated with N(H2) without saturation. Radiative transfer models are able to fit the sub-millimetre data with any of the tested dust models. However, these predict an NIR extinction that is higher and an NIR surface brightness that is lower than based on NIR observations. If the dust sub-millimetre emissivity is rescaled to the observed value of τ(250 μm)∕τ(J), dust models with high NIR albedo can reach the observed level of NIR surface brightness. The NIR extinction of the models tends to be higher than in the direct extinction measurements, which is also reflected in the shape of the NIR surface brightness spectra.
Conclusions. The combination of emission, extinction, and scattering measurements provides strong constraints on dust models. The observations of LDN 1642 indicate clear dust evolution, including a strong increase in the sub-millimetre emissivity, which has not been fully explained by the current dust models yet.
Flares in open clusters with K2
Authors: Ilin Ekaterina , Schmidt Sarah J. , Poppenhäger Katja , Davenport James R. A. , Kristiansen Martti H. , Omohundro Mark 
Published: October 2020

Context. Magnetic fields are a key component in the main sequence evolution of low mass stars. Flares, energetic eruptions on the surfaces of stars, are an unmistakable manifestation of magnetically driven emission. The occurrence rates and energy distributions of flares trace stellar characteristics such as mass and age. However, before flares can be used to constrain stellar properties, the flaring-age-mass relation requires proper calibration.
Aims. This work sets out to quantify the flaring activity of independently age-dated main sequence stars for a broad range of spectral types using optical light curves obtained by the Kepler satellite.
Methods. Drawing from the complete K2 archive, we searched 3435 ∼80 day long light curves of 2111 open cluster members for flares using the open-source software packages K2SC to remove instrumental and astrophysical variability from K2 light curves, and AltaiPony to search and characterize the flare candidates.
Results. We confirmed a total of 3844 flares on high probability open cluster members with ages from zero age main sequence (Pleiades) to 3.6 Gyr (M 67). We extended the mass range probed in the first study of this series to span from Sun-like stars to mid-M dwarfs. We added the Hyades (690 Myr) to the sample as a comparison cluster to Praesepe (750 Myr), the 2.6 Gyr old Ruprecht 147, and several hundred light curves from the late K2 Campaigns in the remaining clusters. We found that the flare energy distribution was similar in the entire parameter space, following a power law relation with exponent α ≈ 1.84−2.39.
Conclusions. We confirm that flaring rates decline with age, and decline faster for higher mass stars. Our results are in good agreement with most previous statistical flare studies. We find evidence that a rapid decline in flaring activity occurred in M1–M2 dwarfs around the ages of the Hyades and Praesepe, when these stars spun down to rotation periods of about 10 d, while higher mass stars had already transitioned to lower flaring rates and lower mass stars still resided in the saturated activity regime. We conclude that some discrepancies between our results and flare studies that used rotation periods for their age estimates could be explained by sample selection bias toward more active stars, but others may point to the limitations of using rotation as an age indicator without additional constraints from stellar activity.
Anterior Cruciate Ligament Reconstructed Female Athletes Exhibit Relative Muscle Dysfunction After Return to Sport
Authors: Raymond-Pope Christiana J. , Dengel Donald R. , Fitzgerald John S. , Nelson Bradley J. , Bosch Tyler A. 
Published: October 2020

AbstractWe sought to examine the relationship between upper-leg compartmental lean mass, muscle-specific strength, and explosive strength following anterior cruciate ligament reconstruction. Twleve adolescent female athletes with prior anterior cruciate ligament reconstruction were individually-matched by age (16.4±0.9 vs. 16.4±1.0 yrs.), body mass index (23.2±2.1 vs. 23.2±2.7 kg/m2), and sport to 12 female athlete controls. One total-body and 2 lateral-leg dual X-ray absorptiometry scans measured total/segmental body composition. Isokinetic dynamometry measured knee extensor/flexor peak torque. Squat jumps on force platforms measured bilateral peak vertical ground reaction force. Paired t-tests assessed lean mass, peak torque, and force between previously-injured athletes’ legs and between previously-injured and control athletes’ legs. Previously-injured athletes’ involved vs. non-involved leg demonstrated lower total (7.13±0.75 vs. 7.43±0.99 kg; p<0.01) and anterior (1.49±0.27 vs. 1.61±0.23 kg; p<0.01) and posterior (1.90±0.19 vs. 2.02±0.21 kg; p=0.04) upper-leg lean mass. Involved leg peak torque (1.36±0.31; 1.06±0.27; 0.97±0.19 Nm/kg) was lower vs. non-involved leg (1.71±0.36; 1.24±0.33; 1.04±0.15 Nm/kg; p<0.01−0.02) for extension at 60 and 120°/sec and flexion at 60°/sec and vs. controls’ ‘matched’ leg (1.77±0.40 Nm/kg; p=0.01) for extension at 60°/sec. Involved leg force (296±45N) was lower vs. non-involved leg (375±55N; p<0.01) and vs. controls’ ‘matched’ leg (372±88N; p=0.02). One-year post-anterior cruciate ligament reconstruction, adolescent female athletes’ involved leg demonstrated relative muscle dysfunction.
Synthesis of Selenopyrano[2,3-c]pyrazol-4(1H)-ones and Their C–H Activation
Authors: Jalani Hitesh B. , Jeong Jin-Hyun , Choi In-Hui 
Published: October 2020

AbstractWe disclose the synthesis of selenopyrano[2,3-c]pyrazol-4(1H)-ones and their aryl derivatives for the first time by using selenopyran ring formation via an in situ-generated selenide that reacts directly with α-halo-β-ynone-bearing substituted pyrazoles to provide the corresponding selenopyrano[2,3-c]pyrazol-4(1H)-ones. Subsequent direct C–H arylation of the latter compounds effected by palladium-catalyzed Heck reactions permits the incorporation of arene substituents onto the selenopyrano[2,3-c]pyrazol-4(1H)-ones scaffolds with moderate to good yields, and might be useful for biological screenings.
Spectral triangles of non-selfadjoint Hill and Dirac operators
Authors: Djakov P. B. , Mityagin B. S. 
Published: October 2020

Abstract
This is a survey of results from the last 10 to 12 years about the structure of the spectra of Hill–Schrödinger and Dirac operators. Let

be a Hill operator or a one-dimensional Dirac operator on the interval

. If

is considered with Dirichlet, periodic, or antiperiodic boundary conditions, then the corresponding spectra are discrete and, for sufficiently large

, close to

in the Hill case or close to

in the Dirac case (

). There is one Dirichlet eigenvalue

and two periodic (if

is even) or antiperiodic (if

is odd) eigenvalues

and

(counted with multiplicity). Asymptotic estimates are given for the spectral gaps

and the deviations

in terms of the Fourier coefficients of the potentials. Moreover, precise asymptotic expressions for

and

are found for special potentials that are trigonometric polynomials.
Bibliography: 45 titles.
Visualization of the HIV-1 Env glycan shield across scales
Authors: Berndsen Zachary T. , Chakraborty Srirupa , Wang Xiaoning , Cottrell Christopher A. , Torres Jonathan L. , Diedrich Jolene K. , López Cesar A. , Yates John R. , van Gils Marit J. , Paulson James C. , Gnanakaran Sandrasegaram , Ward Andrew B. 
Published: October 2020

Significance
The HIV-1 Env “glycan shield” masks the surface of the protein from immune recognition, yet intrinsic heterogeneity defies a typical structure–function description. Using an integrated approach of cryo-EM, computational modeling, and mass spectrometry, we visualized the glycan shield structure in a new light. Our approach facilitated development of cryo-EM analysis methods and allowed for validation of models against experiment. Comparison of Env expressed in different cell lines revealed how subtle differences in composition impact glycan shield structure and affect the accessibility of epitopes on the surface, providing insights for vaccine design. Finally, time-resolved cryo-EM experiments uncovered how highly connected glycan clusters help stabilize the prefusion trimer, suggesting the glycan shield may function beyond immune evasion.
Mcl-1 and Bok transmembrane domains: Unexpected players in the modulation of apoptosis
Authors: Lucendo Estefanía , Sancho Mónica , Lolicato Fabio , Javanainen Matti , Kulig Waldemar , Leiva Diego , Duart Gerard , Andreu-Fernández Vicente , Mingarro Ismael , Orzáez Mar 
Published: October 2020

Significance
Key members of the Bcl-2 family of proteins that control cell death possess a carboxy-terminal transmembrane segment that contributes to subcellular localization and modulates apoptotic functions. The role of Mcl-1 and specially Bok proteins remains elusive. We reveal that the coexpression of Mcl-1 and Bok TMDs produces an increase in the number of ER mitochondrial-associated membranes (MAMs). Furthermore, our findings provide mechanistic insight into the interaction between Mcl-1 and Bok transmembrane domains that can be envisioned as a target for therapeutic intervention.
Reversible autoinhibitory regulation of
Escherichia coli
metallopeptidase BepA for selective β-barrel protein degradation
Authors: Daimon Yasushi , Narita Shin-ichiro , Miyazaki Ryoji , Hizukuri Yohei , Mori Hiroyuki , Tanaka Yoshiki , Tsukazaki Tomoya , Akiyama Yoshinori 
Published: October 2020

Significance
The outer membrane (OM) of gram-negative bacteria functions as a permeability barrier against xenobiotics and is essential for their viability. The periplasmic zinc-metallopeptidase BepA maintains the integrity of the OM by either promoting the assembly of LptD, a β-barrel component of the lipopolysaccharide translocon in the OM, or degrading it when its correct assembly is compromised. How BepA uses its dual functions properly and exerts its protease activity specifically against LptD to be degraded has been unknown. This study shows that the activity of BepA is regulated by reversible autoinhibition mediated by His-246 that acts as the fourth zinc ligand. These findings provide insights into the regulation of metallopeptidases and the quality control of bacterial outer-membrane proteins.
Origin of exponential growth in nonlinear reaction networks
Authors: Lin Wei-Hsiang , Kussell Edo , Young Lai-Sang , Jacobs-Wagner Christine 
Published: October 2020

Significance
Natural systems (e.g., cells and ecosystems) generally consist of reaction networks (e.g., metabolic networks or food webs) with nonlinear flux functions (e.g., Michaelis–Menten kinetics and density-dependent selection). Despite their complex nonlinearities, these systems often exhibit simple exponential growth in the long term. How exponential growth emerges from nonlinear networks remains elusive. Our work demonstrates mathematically how two principles, multivariate scalability of flux functions and ergodicity of the rescaled system, guarantee a well-defined growth rate. By connecting ergodic theory, a powerful branch of mathematics, to the study of growth in biology, our theoretical framework can recapitulate various growth modalities (from balanced growth to periodic, quasi-periodic, or even chaotic behaviors), greatly expanding the types of growing systems that can be studied.