bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain
Authors: Joglekar Anoushka , Prjibelski Andrey , Mahfouz Ahmed , Collier Paul , Lin Susan , Schlusche Anna Katharina , Marrocco Jordan , Williams Stephen R. , Haase Bettina , Hayes Ashley , Chew Jennifer G. , Weisenfeld Neil I. , Wong Man Ying , Stein Alexander N. , Hardwick Simon A. , Hunt Toby , Wang Qi , Dieterich Christoph , Bent Zachary , Fedrigo Olivier , Sloan Steven A. , Risso Davide , Jarvis Erich D. , Flicek Paul , Luo Wenjie , Pitt Geoffrey S. , Frankish Adam , Smit August B. , Ross M. Elizabeth , Tilgner Hagen U. 
Published: January 2021

AbstractSplicing varies across brain regions, but the single-cell resolution of regional variation is unclear. We present a single-cell investigation of differential isoform expression (DIE) between brain regions using single-cell long-read sequencing in mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7 (www.isoformAtlas.com). Isoform tests for DIE show better performance than exon tests. We detect hundreds of DIE events traceable to cell types, often corresponding to functionally distinct protein isoforms. Mostly, one cell type is responsible for brain-region specific DIE. However, for fewer genes, multiple cell types influence DIE. Thus, regional identity can, although rarely, override cell-type specificity. Cell types indigenous to one anatomic structure display distinctive DIE, e.g. the choroid plexus epithelium manifests distinct transcription-start-site usage. Spatial transcriptomics and long-read sequencing yield a spatially resolved splicing map. Our methods quantify isoform expression with cell-type and spatial resolution and it contributes to further our understanding of how the brain integrates molecular and cellular complexity.
Interstitial boron-doped mesoporous semiconductor oxides for ultratransparent energy storage
Authors: Zhi Jian , Zhou Min , Zhang Zhen , Reiser Oliver , Huang Fuqiang 
Published: January 2021

AbstractRealizing transparent and energy-dense supercapacitor is highly challenging, as there is a trade-off between energy storing capability and transparency in the active material film. We report here that interstitial boron-doped mesoporous semiconductor oxide shows exceptional electrochemical capacitance which rivals other pseudocapacitive materials, while maintaining its transparent characteristic. This improvement is credited to the robust redox reactions at interstitial boron-associated defects that transform inert semiconductor oxides into an electrochemically active material without affecting its transparency. By precisely tuning the level of doping, the pseudocapacitive reactivity of these materials is optimized, resulting in a volumetric capacitance up to 1172 F cm−3. Attributing to such efficient charge storage utilization on the active film, the fabricated transparent supercapacitor delivers a maximum areal energy density of 1.36 × 10−3 mWh cm−2 that is close to those of conventional pseudocapacitive materials, with nearly 100% capacitance retention after 15000 cycles and ultrahigh transparency (up to 85% transmittance at 550 nm). In addition, this device shows excellent durability and flexibility with multiple optional outputs, demonstrating the potential as a transparent energy supply in planar electronics.
The multi-photon induced Fano effect
Authors: Litvinenko K. L. , Le Nguyen H. , Redlich B. , Pidgeon C. R. , Abrosimov N. V. , Andreev Y. , Huang Zhiming , Murdin B. N. 
Published: January 2021

AbstractThe ordinary Fano effect occurs in many-electron atoms and requires an autoionizing state. With such a state, photo-ionization may proceed via pathways that interfere, and the characteristic asymmetric resonance structures appear in the continuum. Here we demonstrate that Fano structure may also be induced without need of auto-ionization, by dressing the continuum with an ordinary bound state in any atom by a coupling laser. Using multi-photon processes gives complete, ultra-fast control over the interference. We show that a line-shape indexqnear unity (maximum asymmetry) may be produced in hydrogenic silicon donors with a relatively weak beam. Since the Fano lineshape has both constructive and destructive interference, the laser control opens the possibility of state-selective detection with enhancement on one side of resonance and invisibility on the other. We discuss a variety of atomic and molecular spectroscopies, and in the case of silicon donors we provide a calculation for a qubit readout application.
Crossover between the adiabatic and nonadiabatic electron transfer limits in the Landau-Zener model
Authors: Zhu Guang Yuan , Qin Yi , Meng Miao , Mallick Suman , Gao Hang , Chen Xiaoli , Cheng Tao , Tan Ying Ning , Xiao Xuan , Han Mei Juan , Sun Mei Fang , Liu Chun Y. 
Published: January 2021

AbstractThe semiclassical models of nonadiabatic transition were proposed first by Landau and Zener in 1932, and have been widely used in the study of electron transfer (ET); however, experimental demonstration of the Landau-Zener formula remains challenging to observe. Herein, employing the Hush-Marcus theory, thermal ET in mixed-valence complexes {[Mo2]-(ph)n-[Mo2]}+(n = 1–3) has been investigated, spanning the nonadiabatic throughout the adiabatic limit, by analysis of the intervalence transition absorbances. Evidently, the Landau-Zener formula is valid in the adiabatic regime in a broader range of conditions than the theoretical limitation known as the narrow avoided-crossing. The intermediate system is identified with an overall transition probability (κel) of ∼0.5, which is contributed by the single and the first multiple passage. This study shows that in the intermediate regime, the ET kinetic results derived from the adiabatic and nonadiabatic formalisms are nearly identical, in accordance with the Landau-Zener model. The obtained insights help to understand and control the ET processes in biological and chemical systems.
Epidermal progenitors suppress GRHL3-mediated differentiation through intronic polyadenylation promoted by CPSF-HNRNPA3 collaboration
Authors: Chen Xin , Lloyd Sarah M. , Kweon Junghun , Gamalong Giovanni M. , Bao Xiaomin 
Published: January 2021

AbstractIn self-renewing somatic tissue such as skin epidermis, terminal differentiation genes must be suppressed in progenitors to sustain regenerative capacity. Here we show that hundreds of intronic polyadenylation (IpA) sites are differentially used during keratinocyte differentiation, which is accompanied by downregulation of the Cleavage and Polyadenylation Specificity Factor (CPSF) complex. Sustained CPSF expression in undifferentiated keratinocytes requires the contribution from the transcription factor MYC. In keratinocytes cultured in undifferentiation condition, CSPF knockdown induces premature differentiation and partially affects dynamically used IpA sites. These sites include an IpA site located in the first intron of the differentiation activator GRHL3. CRISPR knockout of GRHL3 IpA increased full-length GRHL3 mRNA expression. Using a targeted genetic screen, we identify that HNRNPA3 interacts with CPSF and enhances GRHL3 IpA. Our data suggest a model where the interaction between CPSF and RNA-binding proteins, such as HNRNPA3, promotes site-specific IpA and suppresses premature differentiation in progenitors.
Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy
Authors: Alteri Claudia , Cento Valeria , Piralla Antonio , Costabile Valentino , Tallarita Monica , Colagrossi Luna , Renica Silvia , Giardina Federica , Novazzi Federica , Gaiarsa Stefano , Matarazzo Elisa , Antonello Maria , Vismara Chiara , Fumagalli Roberto , Epis Oscar Massimiliano , Puoti Massimo , Perno Carlo Federico , Baldanti Fausto 
Published: January 2021

AbstractFrom February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide. By analyzing 346 whole SARS-CoV-2 genomes, we demonstrate the presence of seven viral lineages in Lombardy, frequently sustained by local transmission chains and at least two likely to have originated in Italy. Six single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. The seven lineages, and the presence of local transmission clusters within three of them, revealed that sustained community transmission was underway before the first COVID-19 case had been detected in Lombardy.
Recruitment of upper-limb motoneurons with epidural electrical stimulation of the cervical spinal cord
Authors: Greiner Nathan , Barra Beatrice , Schiavone Giuseppe , Lorach Henri , James Nicholas , Conti Sara , Kaeser Melanie , Fallegger Florian , Borgognon Simon , Lacour Stéphanie , Bloch Jocelyne , Courtine Grégoire , Capogrosso Marco 
Published: January 2021

AbstractEpidural electrical stimulation (EES) of lumbosacral sensorimotor circuits improves leg motor control in animals and humans with spinal cord injury (SCI). Upper-limb motor control involves similar circuits, located in the cervical spinal cord, suggesting that EES could also improve arm and hand movements after quadriplegia. However, the ability of cervical EES to selectively modulate specific upper-limb motor nuclei remains unclear. Here, we combined a computational model of the cervical spinal cord with experiments in macaque monkeys to explore the mechanisms of upper-limb motoneuron recruitment with EES and characterize the selectivity of cervical interfaces. We show that lateral electrodes produce a segmental recruitment of arm motoneurons mediated by the direct activation of sensory afferents, and that muscle responses to EES are modulated during movement. Intraoperative recordings suggested similar properties in humans at rest. These modelling and experimental results can be applied for the development of neurotechnologies designed for the improvement of arm and hand control in humans with quadriplegia.
Degradation of complex arabinoxylans by human colonic Bacteroidetes
Authors: Pereira Gabriel V. , Abdel-Hamid Ahmed M. , Dutta Soumajit , D’Alessandro-Gabazza Corina N. , Wefers Daniel , Farris Jacob A. , Bajaj Shiv , Wawrzak Zdzislaw , Atomi Haruyuki , Mackie Roderick I. , Gabazza Esteban C. , Shukla Diwakar , Koropatkin Nicole M. , Cann Isaac 
Published: January 2021

AbstractSome Bacteroidetes and other human colonic bacteria can degrade arabinoxylans, common polysaccharides found in dietary fiber. Previous work has identified gene clusters (polysaccharide-utilization loci, PULs) for degradation of simple arabinoxylans. However, the degradation of complex arabinoxylans (containing side chains such as ferulic acid, a phenolic compound) is poorly understood. Here, we identify a PUL that encodes multiple esterases for degradation of complex arabinoxylans inBacteroidesspecies. The PUL is specifically upregulated in the presence of complex arabinoxylans. We characterize some of the esterases biochemically and structurally, and show that they release ferulic acid from complex arabinoxylans. Growth of four different colonic Bacteroidetes members, includingBacteroides intestinalis, on complex arabinoxylans results in accumulation of ferulic acid, a compound known to have antioxidative and immunomodulatory properties.
A real-world longitudinal study of anemia management in non-dialysis-dependent chronic kidney disease patients: a multinational analysis of CKDopps
Authors: Lopes Marcelo Barreto , Tu Charlotte , Zee Jarcy , Guedes Murilo , Pisoni Ronald L. , Robinson Bruce M. , Foote Bryce , Hedman Katarina , James Glen , Lopes Antonio Alberto , Massy Ziad , Reichel Helmut , Sloand James , Waechter Sandra , Wong Michelle M. Y. , Pecoits-Filho Roberto 
Published: January 2021

AbstractPreviously lacking in the literature, we describe longitudinal patterns of anemia prescriptions for non-dialysis-dependent chronic kidney disease (NDD-CKD) patients under nephrologist care. We analyzed data from 2818 Stage 3-5 NDD-CKD patients from Brazil, Germany, and the US, naïve to anemia medications (oral iron, intravenous [IV] iron, or erythropoiesis stimulating agent [ESA]) at enrollment in the CKDopps. We report the cumulative incidence function (CIF) of medication initiation stratified by baseline characteristics. Even in patients with hemoglobin (Hb) < 10 g/dL, the CIF at 12 months for any anemia medication was 40%, and 28% for ESAs. Patients with TSAT < 20% had a CIF of 26% and 6% for oral and IV iron, respectively. Heart failure was associated with earlier initiation of anemia medications. IV iron was prescribed to < 10% of patients with iron deficiency. Only 40% of patients with Hb < 10 g/dL received any anemia medication within a year. Discontinuation of anemia treatment was very common. Anemia treatment is initiated in a limited number of NDD-CKD patients, even in those with guideline-based indications to treat. Hemoglobin trajectory and a history of heart failure appear to guide treatment start. These results support the concept that anemia is sub-optimally managed among NDD-CKD patients in the real-world setting.
2D materials coated on etched optical fibers as humidity sensor
Authors: Owji Erfan , Mokhtari Hossein , Ostovari Fatemeh , Darazereshki Behnam , Shakiba Nazanin 
Published: January 2021

AbstractIn this investigation, etched-fibers are coated by 2D layers such as Molybdenum disulfide (MoS2), Molybdenum diselenide (MoSe2) and composition of graphene and graphene oxide (G/GO) to modify humidity sensing. The relative differentiation of attenuations (RDA) in presence of relative humidity (RH) is measured by Optical Loss Test Set at two standard-wavelengths-telecommunication (1310 nm and 1550 nm). Results show that the etched single-mode fiber (ESMF) coated with G/GO has relatively high and one by one function for RDA versus RH (more than 30%). Also, its sensitivity and variance are reasonable. The MoSe2 based sensor is applicable at humidity below 30% because of higher RDA. However, it is not useful at humidity more than 30% due to the absence of one by one function for RDA versus RH. Besides, ESMF coated with MoS2 has indistinctive behavior and is not useful as a humidity sensor.
Mechanistic basis of breast cancer resistance protein inhibition by new indeno[1,2-b]indoles
Authors: Kita Diogo Henrique , Guragossian Nathalie , Zattoni Ingrid Fatima , Moure Vivian Rotuno , Rego Fabiane Gomes de Moraes , Lusvarghi Sabrina , Moulenat Thomas , Belhani Billel , Picheth Geraldo , Bouacida Sofiane , Bouaziz Zouhair , Marminon Christelle , Berredjem Malika , Jose Joachim , Gonçalves Marcos Brown , Ambudkar Suresh V. , Valdameri Glaucio , Le Borgne Marc 
Published: January 2021

AbstractThe ATP-binding cassette transporter ABCG2 mediates the efflux of several chemotherapeutic drugs, contributing to the development of multidrug resistance (MDR) in many cancers. The most promising strategy to overcome ABCG2-mediated MDR is the use of specific inhibitors. Despite many efforts, the identification of new potent and specific ABCG2 inhibitors remains urgent. In this study, a structural optimization of indeno[1,2-b]indole was performed and a new generation of 18 compounds was synthesized and tested as ABCG2 inhibitors. Most compounds showed ABCG2 inhibition with IC50 values below 0.5 µM. The ratio between cytotoxicity (IG50) and ABCG2 inhibition potency (IC50) was used to identify the best inhibitors. In addition, it was observed that some indeno[1,2-b]indole derivatives produced complete inhibition, while others only partially inhibited the transport function of ABCG2. All indeno[1,2-b]indole derivatives are not transported by ABCG2, and even the partial inhibitors are able to fully chemosensitize cancer cells overexpressing ABCG2. The high affinity of these indeno[1,2-b]indole derivatives was confirmed by the strong stimulatory effect on ABCG2 ATPase activity. These compounds did not affect the binding of conformation-sensitive antibody 5D3 binding, but stabilized the protein structure, as revealed by the thermostabilization assay. Finally, a docking study showed the indeno[1,2-b]indole derivatives share the same binding site as the substrate estrone-3-sulfate.
Effects of knee osteoarthritis severity on inter-joint coordination and gait variability as measured by hip-knee cyclograms
Authors: Park Jae Hyeon , Lee Hyojin , Cho Jae-sung , Kim Inyoung , Lee Jongshill , Jang Seong Ho 
Published: January 2021

AbstractInter-joint coordination and gait variability in knee osteoarthritis (KOA) has not been well investigated. Hip-knee cyclograms can visualize the relationship between the hip and knee joint simultaneously. The aim of this study was to elucidate differences in inter-joint coordination and gait variability with respect to KOA severity using hip-knee cyclograms. Fifty participants with KOA (early KOA, n = 20; advanced KOA, n = 30) and 26 participants (≥ 50 years) without KOA were recruited. We analyzed inter-joint coordination by hip-knee cyclogram parameters including range of motion (RoM), center of mass (CoM), perimeter, and area. Gait variability was assessed by the coefficient of variance (CV) of hip-knee cyclogram parameters. Knee RoM was significantly reduced and total perimeter tended to be decreased with KOA progression. KOA patients (both early and advanced) had reduced stance phase perimeter, swing phase area, and total area than controls. Reduced knee CoM and swing phase perimeter were observed only in advanced KOA. Both KOA groups had a greater CV for CoM, knee RoM, perimeter (stance phase, swing phase and total) and swing phase area than the controls. Increased CV of hip RoM was only observed in advanced KOA. These results demonstrate that hip-knee cyclograms can provide insights into KOA patient gait.
Impact of genetic variants on major bleeding after percutaneous coronary intervention based on a prospective multicenter registry
Authors: Cha Jung-Joon , Joo Hyung Joon , Park Jae Hyoung , Hong Soon Jun , Ahn Tae Hoon , Kim Byeong-Keuk , Shin WonYong , Ahn Sung Gyun , Yoon JungHan , Kim Yong Hoon , Cho Yun-Hyeong , Kang Woong Chol , Kim Weon , Lim Young-Hyo , Gwon HyeonCheol , Choi WoongGil , Lim Do-Sun 
Published: January 2021

AbstractAlthough dual antiplatelet therapy is essential for patients who undergo percutaneous coronary interventions, the risk of bleeding remains an unsolved problem, and there is limited information on the potential relationship between genetic variants and major bleeding. We analyzed the correlations between four major single nucleotide polymorphisms (CYP2C19, ABCB1, PON1, and P2Y12 G52T polymorphisms) and clinical outcomes in 4489 patients from a prospective multicenter registry. The primary endpoint was major bleeding, defined as a Bleeding Academic Research Consortium ≥ 3 bleeding event. The allelic frequencies of ABCB1, PON1, and both individual and combined CYP2C19 variants did not differ significantly between patient groups with and without major bleeding. However, the allelic frequency of the P2Y12 variant differed significantly between the two groups. Focusing on the P2Y12 G52T variant, patients in the TT group had a significantly higher rate of major bleeding (6.4%; adjusted hazard ratio [HR] 2.51; 95% confidence interval [CI] 1.08–5.84; p = 0.033) than patients in the other groups (GG [2.9%] or GT [1.9%]). Therefore, the TT variant of the P2Y12 G52T polymorphism may be an independent predictor of major bleeding.Trial registration: NCT02707445 (https://clinicaltrials.gov/ct2/show/NCT02707445?term=02707445&draw=2&rank=1).
Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples
Authors: Alekseenko Alisa , Barrett Donal , Pareja-Sanchez Yerma , Howard Rebecca J. , Strandback Emilia , Ampah-Korsah Henry , Rovšnik Urška , Zuniga-Veliz Silvia , Klenov Alexander , Malloo Jayshna , Ye Shenglong , Liu Xiyang , Reinius Björn , Elsässer Simon J. , Nyman Tomas , Sandh Gustaf , Yin Xiushan , Pelechano Vicent 
Published: January 2021

AbstractRT-LAMP detection of SARS-CoV-2 has been shown to be a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validate the optimized RT-LAMP assay for the detection of SARS-CoV-2 in unextracted heat-inactivated nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large scale testing cannot be met by commercial alternatives.
Chronic exposure of humans to high level natural background radiation leads to robust expression of protective stress response proteins
Authors: Nishad S. , Chauhan Pankaj Kumar , Sowdhamini R. , Ghosh Anu 
Published: January 2021

AbstractUnderstanding exposures to low doses of ionizing radiation are relevant since most environmental, diagnostic radiology and occupational exposures lie in this region. However, the molecular mechanisms that drive cellular responses at these doses, and the subsequent health outcomes, remain unclear. A local monazite-rich high level natural radiation area (HLNRA) in the state of Kerala on the south-west coast of Indian subcontinent show radiation doses extending from ≤ 1 to ≥ 45 mGy/y and thus, serve as a model resource to understand low dose mechanisms directly on healthy humans. We performed quantitative discovery proteomics based on multiplexed isobaric tags (iTRAQ) coupled with LC–MS/MS on human peripheral blood mononuclear cells from HLNRA individuals. Several proteins involved in diverse biological processes such as DNA repair, RNA processing, chromatin modifications and cytoskeletal organization showed distinct expression in HLNRA individuals, suggestive of both recovery and adaptation to low dose radiation. In protein–protein interaction (PPI) networks, YWHAZ (14-3-3ζ) emerged as the top-most hub protein that may direct phosphorylation driven pro-survival cellular processes against radiation stress. PPI networks also identified an integral role for the cytoskeletal protein ACTB, signaling protein PRKACA; and the molecular chaperone HSPA8. The data will allow better integration of radiation biology and epidemiology for risk assessment [Data are available via ProteomeXchange with identifier PXD022380].