bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distillation of Gaussian Einstein-Podolsky-Rosen steering with noiseless linear amplification
Authors: Liu Yang , Zheng Kaimin , Kang Haijun , Han Dongmei , Wang Meihong , Zhang Lijian , Su Xiaolong , Peng Kunchi 
Published: April 2022

AbstractEinstein–Podolsky–Rosen (EPR) steering is one of the most intriguing features of quantum mechanics and an important resource for quantum communication. For practical applications, it remains a challenge to protect EPR steering from decoherence due to its intrinsic difference from entanglement. Here, we experimentally demonstrate the distillation of Gaussian EPR steering and entanglement in lossy and noisy environments using measurement-based noiseless linear amplification. Different from entanglement distillation, the extension of steerable region happens in the distillation of EPR steering, besides the enhancement of steerabilities. We demonstrate that the two-way or one-way steerable region is extended after the distillation of EPR steering when the NLA is implemented based on Bob’s or Alice’s measurement results. We also show that the NLA helps to extract the secret key from the insecure region in one-sided device-independent quantum key distribution with EPR steering. Our work paves the way for quantum communication exploiting EPR steering in practical quantum channels.
Structural basis of tethered agonism of the adhesion GPCRs ADGRD1 and ADGRF1
Authors: Qu Xiangli , Qiu Na , Wang Mu , Zhang Bingjie , Du Juan , Zhong Zhiwei , Xu Wei , Chu Xiaojing , Ma Limin , Yi Cuiying , Han Shuo , Shui Wenqing , Zhao Qiang , Wu Beili 
Published: April 2022

AbstractAdhesion G protein-coupled receptors (aGPCRs) are essential for a variety of physiological processes such as immune responses, organ development, cellular communication, proliferation and homeostasis1–7. An intrinsic manner of activation that involves a tethered agonist in the N-terminal region of the receptor has been proposed for the aGPCRs8,9, but its molecular mechanism remains elusive. Here we report the G protein-bound structures of ADGRD1 and ADGRF1, which exhibit many unique features with regard to the tethered agonism. The stalk region that proceeds the first transmembrane helix acts as the tethered agonist by forming extensive interactions with the transmembrane domain; these interactions are mostly conserved in ADGRD1 and ADGRF1, suggesting that a common stalk–transmembrane domain interaction pattern is shared by members of the aGPCR family. A similar stalk binding mode is observed in the structure of autoproteolysis-deficient ADGRF1, supporting a cleavage-independent manner of receptor activation. The stalk-induced activation is facilitated by a cascade of inter-helix interaction cores that are conserved in positions but show sequence variability in these two aGPCRs. Furthermore, the intracellular region of ADGRF1 contains a specific lipid-binding site, which proves to be functionally important and may serve as the recognition site for the previously discovered endogenous ADGRF1 ligand synaptamide. These findings highlight the diversity and complexity of the signal transduction mechanisms of the aGPCRs.
The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community
Authors: Nissa Mehar Un , Reddy Panga Jaipal , Pinto Nevil , Sun Zhi , Ghosh Biplab , Moritz Robert L. , Goswami Mukunda , Srivastava Sanjeeva 
Published: April 2022

AbstractLabeo rohita (Rohu) is one of the most important fish species produced in world aquaculture. Integrative omics research provides a strong platform to understand the basic biology and translate this knowledge into sustainable solutions in tackling disease outbreak, increasing productivity and ensuring food security. Mass spectrometry-based proteomics has provided insights to understand the biology in a new direction. Very little proteomics work has been done on ‘Rohu’ limiting such resources for the aquaculture community. Here, we utilised an extensive mass spectrometry based proteomic profiling data of 17 histologically normal tissues, plasma and embryo of Rohu to develop an open source PeptideAtlas. The current build of “Rohu PeptideAtlas” has mass-spectrometric evidence for 6015 high confidence canonical proteins at 1% false discovery rate, 2.9 million PSMs and ~150 thousand peptides. This is the first open-source proteomics repository for an aquaculture species. The ‘Rohu PeptideAtlas’ would promote basic and applied aquaculture research to address the most critical challenge of ensuring nutritional security for a growing population.
Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity
Authors: Gong Binsheng , Deveson Ira W. , Mercer Timothy , Johann Donald J. , Jones Wendell , Tong Weida , Xu Joshua 
Published: April 2022

AbstractRecently we reported the accuracy and reproducibility of circulating tumor DNA (ctDNA) assays using a unique set of reference materials, associated analytical framework, and suggested best practices. With the rapid adoption of ctDNA sequencing in precision oncology, it is critical to understand the analytical validity and technical limitations of this cutting-edge and medical-practice-changing technology. The SEQC2 Oncopanel Sequencing Working Group has developed a multi-site, cross-platform study design for evaluating the analytical performance of five industry-leading ctDNA assays. The study used tailor-made reference samples at various levels of input material to assess ctDNA sequencing across 12 participating clinical and research facilities. The generated dataset encompasses multiple key variables, including a broad range of mutation frequencies, sequencing coverage depth, DNA input quantity, etc. It is the most comprehensive public-facing dataset of its kind and provides valuable insights into ultra-deep ctDNA sequencing technology. Eventually the clinical utility of ctDNA assays is required and our proficiency study and corresponding dataset are needed steps towards this goal.
Variation in the ratio of compounds in a plant volatile blend during transmission by wind
Authors: Cai Xiaoming , Guo Yuhang , Bian Lei , Luo Zongxiu , Li Zhaoqun , Xiu Chunli , Fu Nanxia , Chen Zongmao 
Published: April 2022

AbstractFor plant volatiles to mediate interactions in tritrophic systems, they must convey accurate and reliable information to insects. However, it is unknown whether the ratio of compounds in plant volatile blends remains stable during wind transmission. In this study, volatiles released from an odor source were collected at different points in a wind tunnel and analyzed. The variation in the amounts of volatiles collected at different points formed a rough cone shape. The amounts of volatiles collected tended to decrease with increasing distance from the odor source. Principal component analyses showed that the volatile profiles were dissimilar among different collection points. The profiles of volatiles collected nearest the odor source were the most similar to the released odor. Higher wind speed resulted in a clearer spatial distribution of volatile compounds. Thus, variations in the ratios of compounds in odor plumes exist even during transport over short distances.
MicroRNA profiles in aqueous humor between pseudoexfoliation glaucoma and normal tension glaucoma patients in a Korean population
Authors: Cho Hyun-kyung , Seong Hyemin , Kee Changwon , Song Dae Hyun , Kim Seong Jae , Seo Seong Wook , Kang Sang Soo 
Published: April 2022

AbstractWe aimed to obtain microRNA (miRNA) profiles of patients with pseudoexfoliation (PEX) glaucoma or normal-tension glaucoma (NTG) compared to normal controls using individual aqueous humor (AH) samples and investigate the role of miRNAs in the pathogenesis of PEX glaucoma compared to NTG in Korean. AH (80-120 µl) was collected before cataract surgery or trabeculectomy from 26 Korean subjects (eleven with PEX glaucoma, age-matched eight NTG, and seven controls). RNA sequencing was conducted for RNA samples extracted from 26 AH samples. Bioinformatics analysis was performed for targets and related pathways. A total of 334 and 291 discrete miRNAs were detected in AH samples of PEX glaucoma and NTG patients, respectively. Two significantly upregulated miRNAs (hsa-miR-30d-5p and hsa-miR-320a) and ten significantly downregulated miRNAs (hsa-miR-3156-5p, hsa-miR-4458, hsa-miR-6717-5p, hsa-miR-6728-5p, hsa-miR-6834-5p, hsa-miR-6864-5p, hsa-miR-6879-5p, hsa-miR-877-3p, hsa-miR-548e-3p, and hsa-miR-6777-5p) in PEX glaucoma patients compared to control (fold-change > 2, p < 0.05) were found. In NTG patients, ten significantly upregulated and two downregulated miRNAs compared to control were found. Only hsa-miR-6777-5p was commonly downregulated in both PEX glaucoma and NTG patients. Related pathways were proteoglycans in cancer, glioma, and TGF-beta signaling pathway in PEX glaucoma. These differentially expressed miRNAs between PEX glaucoma and NTG samples suggest the possible role of miRNA in the pathogenesis of glaucoma, further implying that pathogenic mechanisms may differ between different types of glaucoma.
Antiplatelet response to clopidogrel is associated with a haplotype in CYP2C19 gene in Pakistani patients
Authors: Ahmed Sagheer , Gul Saima , Siraj Sami , Hussain Abrar , Sheikh Fahad Sultan , Shah Saeed Ullah , Janjua Kholood , Khan Hizbullah , Hamdard Mohammad Hamid 
Published: April 2022

AbstractClopidogrel, an antiplatelet drug, is frequently prescribed to patients diagnosed with ischemic diseases such as those suffering from acute coronary syndromes or ischemic stroke. Despite the drug being effective in majority of the patients, some still experience ischemic events early in the treatment which might be due to poor platelet inhibition. This study aims to investigate the association of cytochrome P450 2C19 (CYP2C19) loss-of-function polymorphisms, haplotypes as well as a wide range of clinical and demographic variables with platelet aggregation phenotypes to clopidogrel in a Pakistani cohort. The study comprised of a total of 120 patients diagnosed with cardiovascular diseases and were treated with clopidogrel. Antiplatelet response to clopidogrel was monitored by Helena AggRAM (HL-2-1785P) and patients with maximal platelet aggregation more than 50% were categorized as low responders and those with less than 50% as high responders. Our results show that 56.6% of patients were homozygous for the CYP2C19 wild-type allele, 38.3% of patients possessed one copy of the CYP2C19*2 allele and 5% of patients possessed both CYP2C19*2 alleles. No CYP2C19*3 allele was found in our patient cohort. There was no statistically significant difference between the high and low responder groups to clopidogrel in terms of extensive, intermediate and poor metabolizer genotypes. However, haplotype (H1), leukocyte count, random blood glucose, and history of diabetes mellitus was associated with the antiplatelet response to clopidogrel. The prevalence of clopidogrel resistance in our population was in line with that reported for other regional and global populations.
Enhanced conductance response in radio frequency scanning tunnelling microscopy
Authors: Wit Bareld , Vranik Radovan , Müllegger Stefan 
Published: April 2022

AbstractDiverse spectroscopic methods operating at radio frequency depend on a reliable calibration to compensate for the frequency dependent damping of the transmission lines. Calibration may be impeded by the existence of a sensitive interdependence of two or more experimental parameters. Here, we show by combined scanning tunnelling microscopy measurements and numerical simulations how a frequency-dependent conductance response is affected by different DC conductance behaviours of the tunnel junction. Distinct and well-defined DC-conductance behaviour is provided by our experimental model systems, which include C60 molecules on Au(111), exhibiting electronic configurations distinct from the well-known dim and bright C60’s reported so far. We investigate specific combinations of experimental parameters. Variations of the modulation amplitude as small as only a few percent may result in systematic conductance deviations as large as one order of magnitude. We provide practical guidelines for calibrating respective measurements, which are relevant to RF spectroscopic measurements.
Algorithmic multiscale analysis for the FcRn mediated regulation of antibody PK in human
Authors: Patsatzis Dimitris G. , Wu Shengjia , Shah Dhaval K. , Goussis Dimitris A. 
Published: April 2022

AbstractA demonstration is provided on how algorithmic asymptotic analysis of multi-scale pharmacokinetics (PK) systems can provide (1) system level understanding and (2) predictions on the response of the model when parameters vary. Being algorithmic, this type of analysis is not hindered by the size or complexity of the model and requires no input from the investigator. The algorithm identifies the constraints that are generated by the fast part of the model and the components of the slow part of the model that drive the system within these constraints. The demonstration is based on a typical monoclonal antibody PK model. It is shown that the findings produced by the traditional methodologies, which require significant input by the investigator, can be produced algorithmically and more accurately. Moreover, additional insights are provided by the algorithm, which cannot be obtained by the traditional methodologies; notably, the dual influence of certain reactions depending on whether their fast or slow component dominates. The analysis reveals that the importance of physiological processes in determining the systemic exposure of monoclonal antibodies (mAb) varies with time. The analysis also confirms that the rate of mAb uptake by the cells, the binding affinity of mAb to neonatal Fc receptor (FcRn), and the intracellular degradation rate of mAb are the most sensitive parameters in determining systemic exposure of mAbs. The algorithmic framework for analysis introduced and the resulting novel insights can be used to engineer antibodies with desired PK properties.
Unusual features of lattice dynamics in lawsonite near its phase transitions
Authors: Kadlec Filip , Nuzhnyy Dmitry , Kadlec Christelle , Petzelt Jan , Savinov Maxim , Kamba Stanislav 
Published: April 2022

AbstractLattice dynamics of a single crystal of lawsonite were studied over a broad range of frequencies (1 Hz to 20 THz) using impedance, THz time-domain and infrared spectroscopies. Based on polarized spectra of complex permittivity $$\hat{\varepsilon }$$

ε
^

measured as a function of temperature between 10 K and 500 K, we analyzed the properties of the two known phase transitions—an antiferrodistortive one near $$T_{\mathrm{c}1}=270\,\mathrm{K}$$

T

c
1

=
270

K

and a ferroelectric one, occurring at $$T_{\mathrm{c}2}=124\,\mathrm{K}$$

T

c
2

=
124

K

. The former one is accompanied by a flat maximum in the THz-range permittivity $$\hat{\varepsilon }_{\mathrm{c}}$$

ε
^

c

near $$T_{\mathrm{c}1}$$

T

c
1

, which is due to an overdamped polar excitation in the $$\mathbf {E} \parallel c$$

E
‖
c

spectra reflecting the dynamics of water and hydroxyl groups. The strength of this mode decreases on cooling below $$T_{\mathrm{c}1}$$

T

c
1

, and the mode vanishes below $$T_{\mathrm{c}2}$$

T

c
2

due to hydrogen ordering. At the pseudoproper ferroelectric phase transition, two independent anomalies in permittivity were observed. First, $$\hat{\varepsilon }_a$$

ε
^

a

exhibits a peak at $$T_{\mathrm{c}2}=124\,\mathrm{K}$$

T

c
2

=
124

K

due to critical slowing down of a relaxation in the GHz range. Second, infrared and THz spectra revealed an optical phonon softening towards $$T_{\mathrm{c}2}$$

T

c
2

which causes a smaller but pronounced maximum in $$\hat{\varepsilon }_b$$

ε
^

b

. Such anomaly, consisting in a soft mode polarized perpendicularly to the ferroelectric axis, is unusual in ferroelectrics.
Antioxidant potential and essential oil properties of Hypericum perforatum L. assessed by application of selenite and nano-selenium
Authors: Nazari Mahmonir Rezaei , Abdossi Vahid , Hargalani Fariba Zamani , Larijani Kambiz 
Published: April 2022

AbstractIt is necessary to develop a simple way to achieve food quality quantitatively. Nanotechnology is a key advanced technology enabling contribution, development, and sustainable impact on food, medicine, and agriculture. In terms of medicinal and therapeutic properties, Hypericumperforatum is an important species. For this study, a randomized complete block design with three replications was used in each experimental unit. The foliar application of selenite and nano-selenium (6, 8, 10, and 12 mg/l), control (distilled water), at the rosette stage and harvesting at 50% flowering stage has been applied as an alleviation strategy subjected to producing essential oils and antioxidant activity. Experimental results revealed that the selenite and nano selenium fertilizers had a significant effect on traits such as total weight of biomass, essential oil percentage, the content of hypericin and hyperforin, the selenium accumulation in the plant, relative leaf water content, chlorophylls, phenolic content, proline, catalase, peroxidase, malondialdehyde, and DPPH. The highest essential oil content was obtained from the control treatment when the accumulation of selenium was achieved with 12 mg/l nano-selenium. The maximum rate of hypericin was seen in the foliar application of 8 mg/l selenite whereas the maximum hyperforin was gained at 10 mg/l selenium. Conceding that the goal is to produce high hypericin/ hyperforin, and also the accumulation of selenium in the plant, treatments of 6 and 8 mg/l of selenite and nano-selenium could be applied. Consequently, an easy detection technique proposed herein can be successfully used in different ranges, including biology, medicine, and the food industry.
Impact of prenatal famine exposure on adulthood fasting blood glucose level
Authors: Abate Kalkidan Hassen , Arage Getachew , Hassen Habtamu , Abafita Jemal , Belachew Tefera 
Published: April 2022

AbstractIn the past decade, in low-income countries, there have been a rapid rise in prevalence of diabetes among adult population. Hence, understanding the context specific drivers of this change including the impacts of childhood nutrition adversaries on adult metabolic conditions is critical undertaking. This study investigates the potential effects of prenatal famine exposure to the Ethiopian great famine (1983–1985) on adulthood blood glucose level of survivors. A total of 441 adults (222 exposed and 219 controls) were included in the study. Self-reported place of birth and, date of birth and/or age were used to identify participants. A multivariable linear regression analysis was used to analyze the impact of prenatal famine exposure on the level of fasting blood glucose. In linear regression, unadjusted model (Model 1), fasting blood glucose level was increased by 4.13 (β = 4.13; 95% CI .41, 7.42) points in prenatal famine exposed groups, compared with non-exposed. Similarly, the positive association of prenatal famine exposure and fasting blood glucose level was maintained after adjusted for sex (Model 2) (β = . 4.08 95% CI .056, 7.50). Further adjusted for age, residence, educational status, wealth index and family size (Model 3) resulted in 4.10 (β = . 4.10 95% CI .45, 7.56) points increases in fasting blood glucose level. In model 4 adjusting for dietary pattern, physical activity level and family history of diabetes, alcohol and cigarette smoking resulted in 3.90 (β = 3.90, 95% CI 039, 7.52) points increase in fasting glucose level. In the he full adjusted model (Model 5) prenatal exposure to famine was resulted in 3.78 (β = 3.78, 95% CI .22, 7.34) increases in fasting blood glucose level after adjusted for BMI and waist to height ratio. There existed a positive association of prenatal famine exposure and adulthood blood glucose levels. In this population, establishing effective overweight/obesity prevention programs to minimize the co-impact of early famine exposure on blood glucose control are important.
The lipophilic cyclic peptide cyclosporin A induces aggregation of gel-forming mucins
Authors: Kishimoto Hisanao , Ridley Caroline , Thornton David J. 
Published: April 2022

AbstractCyclic peptides are good candidates for orally delivered therapeutics, however, issues remain in their development due to low intestinal permeability. Although some of the biological factors have been reported that regulate intestinal permeation of cyclic peptides, the influence of the mucus barrier, a major hurdle to epithelial drug delivery, on cyclic peptide bioavailability is unclear. In this study, we show that the lipophilic cyclic peptide, cyclosporin A (CsA), interacted with, and likely induced aggregation, of polymeric, gel-forming mucins (MUC2, MUC5AC and MUC5B) which underpin the mucus gel-networks in the gastrointestinal tract. Under similar conditions, two other cyclic peptides (daptomycin and polymyxin B) did not cause mucin aggregation. Using rate-zonal centrifugation, purified MUC2, MUC5AC and MUC5B mucins sedimented faster in the presence of CsA, with a significant increase in mucins in the pellet fraction. In contrast, mucin sedimentation profiles were largely unaltered after treatment with daptomycin or polymyxin B. CsA increased MUC5B sedimentation was concentration-dependent, and sedimentation studies using recombinant mucin protein domains suggests CsA most likely causes aggregation of the relatively non-O-glycosylated N-terminal and C-terminal regions of MUC5B. Furthermore, the aggregation of the N-terminal region, but not the C-terminal region, was affected by pH. CsA has partially N-methylated amide groups, this unique molecular structure, not present in daptomycin and polymyxin B, may potentially be involved in interaction with gel-forming mucin. Taken together, our results indicate that the interaction of gel-forming mucins with the cyclic peptide CsA is mediated at the N- and C-terminal domains of mucin polymers under physiological conditions. Our findings demonstrate that the mucus barrier is an important physiological factor regulating the intestinal permeation of cyclic peptides in vivo.