bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tissue-specific endothelial cell heterogeneity contributes to unequal inflammatory responses
Authors: Gunawardana Hasitha , Romero Tahmineh , Yao Ning , Heidt Sebastiaan , Mulder Arend , Elashoff David A. , Valenzuela Nicole M. 
Published: January 2021

AbstractEndothelial cells (EC) coordinate vascular homeostasis and inflammation. In organ transplantation, EC are a direct alloimmune target. We posited that tissue specific heterogeneity of vascular EC may partly underlie the disparate organ-specific alloimmune risk. We examined the vascular endothelial response to inflammation across six primary endothelial beds from four major transplanted organs: the heart, lung, kidney and liver. First, we reanalyzed a public dataset of cardiac allograft rejection and found that endothelial inflammatory response genes were elevated in human cardiac allograft biopsies undergoing rejection compared with stable grafts. Next, the inducible inflammatory phenotypes of EC from heart, lung, kidney, and liver were characterized in vitro, focused on expression of adhesion molecules and chemokines, and recruitment of allogeneic peripheral blood mononuclear immune cells. Large vessel cardiac EC most highly upregulated VCAM-1, particularly compared with hepatic EC, supported greater leukocyte adhesion and had distinct chemokine profiles after stimulation with cytokines and complement. Differentially expressed gene candidates that are known regulators of cytokine signaling and inflammatory programming were verified in publicly available datasets of organ-specific endothelial transcriptomes. In summary, differential baseline expression of immune regulating genes may contribute to differential vascular inflammatory responses depending on organ.
Family graveyards form underappreciated local plant diversity hotspots in China's agricultural landscapes
Authors: Gong Cheng , Li Liangtao , Axmarcher Jan C. , Yu Zhenrong , Liu Yunhui 
Published: January 2021

AbstractIn the intensively farmed, homogenous agricultural landscape of the North China Plain, family graveyards form distinct cultural landscape features. In addition to their cultural value, these graveyards represent semi-natural habitat islands whose potential roles in biodiversity conservation and ecological functioning has remained poorly understood. In this study, we investigated plant species richness on 199 family graveyards of different ages and sizes. In accordance with biogeography theory, both overall and insect-pollinated plant species richness increased with area and age of graveyards. Even small graveyards show a strong potential for conserving local plant richness, and a mosaic of both large and small family graveyards could play an important role in the conservation of farmland biodiversity and related ecosystem functions. The launch of agri-environmental measures that conserve and create semi-natural habitats, in turn benefitting agricultural biodiversity and ecological functioning, has proven difficult in China due to the shortage of dispensable arable land. Given the great value of family graveyards as semi-natural habitats reflected in our study, we propose to focus preliminary efforts on conserving these landscape features as existing, widespread and culturally important semi-natural habitat islands. This would represent an effective, complementary policy to a subsequent re-establishment of other semi-natural habitats for the conservation of biodiversity and ecological functioning in agricultural landscapes.
Deficit saline water irrigation under reduced tillage and residue mulch improves soil health in sorghum-wheat cropping system in semi-arid region
Authors: Soni Pooja Gupta , Basak Nirmalendu , Rai Arvind Kumar , Sundha Parul , Narjary Bhaskar , Kumar Parveen , Yadav Gajender , Kumar Satyendra , Yadav Rajender Kumar 
Published: January 2021

AbstractJudicious application of saline water except for critical growth stages, could be the only practical solution to meet the crop water demand in arid and semi-arid regions, due to limited access to freshwater, especially during dry winter months. A field experiment was conducted to study the effect of tillage [conventional (CT), reduced (RT), and zero (ZT)], rice straw mulch and deficit saline-water irrigation in wheat (100, 80 and 60% of wheat water requirement, CWR) followed by rainfed sorghum on soil properties and the yields of the cropping system. Yields of both the crops were comparable between RT and CT, but the wheat yield was reduced in ZT. The RT, mulching and deficit saline irrigation in wheat season (60% CWR) increased the sorghum fodder yield. Olsen’s P (8.7–20.6%) and NH4OAc-K (2.5–7.5%) increased in RT and ZT, respectively, over CT under both the crops. Deficit irrigation reduced soil salinity (ECe) by 0.73–1.19 dS m−1after each crop cycle, while soil microbial biomass C (MBC) and N (MBN), dehydrogenase, urease and alkaline phosphatase reduced with an increase in ECe. Theα-glucosidase, MBC, ECe, KMnO4oxidizable N, and urease were identified as major contributors in developing the soil health index. Deficit irrigation (60% CWR) and rice straw mulching under ZT and RT showed higher values of soil health index. Overall, deficit saline-water irrigation under reduced tillage and straw mulching had the greatest potential in maintaining soil health, saving fresh irrigation water without affecting the productivity of the sorghum-wheat system in the semi-arid regions of India. Results also demonstrated that salt affected areas of arid and semiarid countries can replicate the protocol for indexing and screening of soil health indicators to assess the sustainability of a cropping system. This integrated management based on the nature of the available resources also provided a practical approach to achieve the target of land degradation neutrality and land restoration.
Sudden sensorineural hearing loss in patients with vestibular schwannoma
Authors: Wasano Koichiro , Oishi Naoki , Noguchi Masaru , Hentona Ko , Shinden Seiichi , Kitama Tsubasa , Tsuzuki Nobuyoshi , Kawasaki Taiji , Hiraga Yoshihiko , Takei Yasuhiko , Ogawa Kaoru 
Published: January 2021

AbstractClinical features of sudden sensorineural hearing loss (SSNHL) associated with vestibular schwannoma (VS) are not fully understood. Determining a treatment plan and explaining it to patients requires clinicians to clearly understand the clinical features related to the tumor, including SSNHL. To identify the full range of clinical features of VS-associated SSNHL, especially recovery of hearing following multiple episodes of SSNHL and what factors predict recovery and recurrence. A multicenter retrospective chart review was conducted in seven tertiary care hospitals between April 1, 2011, and March 31, 2020. We collected and analyzed dose of administered steroid, pure-tone audiometry results, and brain MRIs of patients diagnosed with VS-associated SSNHL. Seventy-seven patients were included. They experienced 109 episodes of audiogram-confirmed SSNHL. The highest proportion of complete recoveries occurred in patients with U-shaped audiograms. The recovery rates for the first, second, and third and subsequent episodes of SSNHL were 53.5%, 28.0%, and 9.1%, respectively. Recovery rate decreased significantly with increasing number of SSNHL episodes (P =0 .0011; Cochran-Armitage test). After the first episode of SSNHL, the recurrence-free rate was 69.9% over 1 year and 57.7% over 2 years; the median recurrence time was 32 months. Logarithmic approximation revealed that there is a 25% probability that SSNHL would recur within a year. SSNHL in patients with VS is likely to recur within one year in 25% of cases. Also, recovery rate decreases as a patient experiences increasing episodes of SSNHL.
The number of osteoclasts in a biopsy specimen can predict the efficacy of neoadjuvant chemotherapy for primary osteosarcoma
Authors: Araki Yoshihiro , Yamamoto Norio , Hayashi Katsuhiro , Takeuchi Akihiko , Miwa Shinji , Igarashi Kentaro , Higuchi Takashi , Abe Kensaku , Taniguchi Yuta , Yonezawa Hirotaka , Morinaga Sei , Asano Yohei , Ikeda Hiroko , Nojima Takayuki , Tsuchiya Hiroyuki 
Published: January 2021

AbstractOsteosarcoma is the most common primary malignant bone tumor, and its standard treatment is a combination of surgery and chemotherapy. A poor response to chemotherapy causes unfavorable oncological outcomes. We investigated the correlation between osteoclast differentiation in biopsy specimens and the efficacy of neoadjuvant chemotherapy in resected specimens. Forty-nine patients who underwent neoadjuvant chemotherapy and subsequent surgical treatment at our institution between 1999 and 2018 were enrolled. Using medical records, we investigated the age, sex, tumor size, location, subtype, staging, chemotherapy agents (doxorubicin, cisplatin, ifosfamide, and methotrexate), number of neoadjuvant chemotherapy courses, number of osteoclasts in biopsy specimens, and efficacy of neoadjuvant chemotherapy according to the Rosen and Huvos classification (Grade I-IV) in resected specimens. Univariate and multivariate analyses were performed to identify factors predictive of a good response in resected specimens after neoadjuvant chemotherapy. A good response (Grade III/IV) was detected in 25, while a poor response (Grade I/II) was detected in 24. According to the multivariate analysis, ≥ 46 years old (odds ratio [OR], 0.05; 95% confidence interval [CI], 0.01–0.45; p < 0.01) and ≥ 5 mature osteoclasts in a biopsy specimen (OR, 36.9; 95% CI, 6.03–225; p < 0.01) were significantly associated with the neoadjuvant chemotherapy efficacy. The accuracy for predicting a good response to chemotherapy based on ≥ 5 osteoclasts in a biopsy specimen in patients < 46 years old was 85%. The number of mature osteoclasts in biopsy specimens is a simple factor for predicting the efficacy of chemotherapy before treatment, although further studies will be required to determine the underlying mechanism.
Reduced sampling rate Kalman filters for carrier phase and frequency offset tracking in 200 Gbps 16 QAM coherent communication system
Authors: Sharma Srishti , Krishnamurthy Pradeep Kumar 
Published: January 2021

AbstractWe propose 1 state and 2 state multi-step Kalman filters (MKFs) to estimate and compensate CFO, LPN and NLPN in long-haul coherent fiber-optic communication systems. The proposed filters generate state estimates once everymsymbols and therefore operate at a reduced sampling rate compared to conventional KFs that perform symbol by symbol processing. No computations are performed to obtain phase estimates of the intermediate$$m-1$$m-1samples; instead, the present and previous estimates are averaged and used to derotate the intermediate$$m-1$$m-1samples which are then demodulated to recover the transmitted symbols. This reduces the computational load on the receiver DSP. Further, in order to improve estimation accuracy, we adaptively vary the process noise covarianceQ. Simulation results of 200 Gbps PDM 16 QAM system over 12 spans shows that the proposed 1 state MKF can reduce the sampling rate requirement by a factor of$$m = 20$$m=20with Q-factor degradation of 1.32 dB compared to single-step KF at linewidth of 100 kHz. The 2 state MKF tracks PN and CFO with a maximum step size of$$m=10$$m=10for a CFO of 100 MHz at linewidth of 100 kHz. We also study the dynamic performance of the proposed algorithms by applying step change to CFO. The 2 state MKF with adaptiveQis able to track a step change of 400 MHz of CFO with$$m = 1$$m=1and 3 with high estimation accuracy but slower convergence time compared to the non-adaptive 2 state MKF. Finally, we study the computational requirements of the proposed MKFs and show that they offer significant reduction in computations compared to single-step KF thus making the proposed filters suitable for hardware implementation.
Antibiotics and the developing intestinal microbiome, metabolome and inflammatory environment in a randomized trial of preterm infants
Authors: Russell Jordan T. , Lauren Ruoss J. , de la Cruz Diomel , Li Nan , Bazacliu Catalina , Patton Laura , McKinley Kelley Lobean , Garrett Timothy J. , Polin Richard A. , Triplett Eric W. , Neu Josef 
Published: January 2021

AbstractAntibiotic use in neonates can have detrimental effects on the developing gut microbiome, increasing the risk of morbidity. A majority of preterm neonates receive antibiotics after birth without clear evidence to guide this practice. Here microbiome, metabolomic, and immune marker results from the routine early antibiotic use in symptomatic preterm Neonates (REASON) study are presented. The REASON study is the first trial to randomize symptomatic preterm neonates to receive or not receive antibiotics in the first 48 h after birth. Using 16S rRNA sequencing of stool samples collected longitudinally for 91 neonates, the effect of such antibiotic use on microbiome diversity is assessed. The results illustrate that type of nutrition shapes the early infant gut microbiome. By integrating data for the gut microbiome, stool metabolites, stool immune markers, and inferred metabolic pathways, an association was discovered betweenVeillonellaand the neurotransmitter gamma-aminobutyric acid (GABA). These results suggest early antibiotic use may impact the gut-brain axis with the potential for consequences in early life development, a finding that needs to be validated in a larger cohort.Trial RegistrationThis project is registered at clinicaltrials.gov under the name “Antibiotic ‘Dysbiosis’ in Preterm Infants” with trial number NCT02784821.
Muscle metabolic remodelling patterns in Duchenne muscular dystrophy revealed by ultra-high-resolution mass spectrometry imaging
Authors: Dabaj Ivana , Ferey Justine , Marguet Florent , Gilard Vianney , Basset Carole , Bahri Youssef , Brehin Anne-Claire , Vanhulle Catherine , Leturcq France , Marret Stéphane , Laquerrière Annie , Schmitz-Afonso Isabelle , Afonso Carlos , Bekri Soumeya , Tebani Abdellah 
Published: January 2021

AbstractDuchenne muscular dystrophy (DMD) is a common and severe X-linked myopathy, characterized by muscle degeneration due to altered or absent dystrophin. DMD has no effective cure, and the underlying molecular mechanisms remain incompletely understood. The aim of this study is to investigate the metabolic changes in DMD using mass spectrometry-based imaging. Nine human muscle biopsies from DMD patients and nine muscle biopsies from control individuals were subjected to untargeted MSI using matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry. Both univariate and pattern recognition techniques have been used for data analysis. This study revealed significant changes in 34 keys metabolites. Seven metabolites were decreased in the Duchenne biopsies compared to control biopsies including adenosine triphosphate, and glycerophosphocholine. The other 27 metabolites were increased in the Duchenne biopsies, including sphingomyelin, phosphatidylcholines, phosphatidic acids and phosphatidylserines. Most of these dysregulated metabolites are tightly related to energy and phospholipid metabolism. This study revealed a deep metabolic remodelling in phospholipids and energy metabolism in DMD. This systems-based approach enabled exploring the metabolism in DMD in an unprecedented holistic and unbiased manner with hypothesis-free strategies.
Bayesian inference of the viscoelastic properties of a Jeffrey’s fluid using optical tweezers
Authors: Paul Shuvojit , Narinder N , Banerjee Ayan , Nayak K Rajesh , Steindl Jakob , Bechinger Clemens 
Published: January 2021

AbstractBayesian inference is a conscientious statistical method which is successfully used in many branches of physics and engineering. Compared to conventional approaches, it makes highly efficient use of information hidden in a measured quantity by predicting the distribution of future data points based on posterior information. Here we apply this method to determine the stress-relaxation time and the solvent and polymer contributions to the frequency dependent viscosity of a viscoelastic Jeffrey’s fluid by the analysis of the measured trajectory of an optically trapped Brownian particle. When comparing the results to those obtained from the auto-correlation function, mean-squared displacement or the power spectrum, we find Bayesian inference to be much more accurate and less affected by systematic errors.
Recording site placement on planar silicon-based probes affects signal quality in acute neuronal recordings
Authors: Fiáth Richárd , Meszéna Domokos , Somogyvári Zoltán , Boda Mihály , Barthó Péter , Ruther Patrick , Ulbert István 
Published: January 2021

AbstractMultisite, silicon-based probes are widely used tools to record the electrical activity of neuronal populations. Several physical features of these devices are designed to improve their recording performance. Here, our goal was to investigate whether the position of recording sites on the silicon shank might affect the quality of the recorded neural signal in acute experiments. Neural recordings obtained with five different types of high-density, single-shank, planar silicon probes from anesthetized rats were analyzed. Wideband data were filtered to extract spiking activity, then the amplitude distribution of samples and quantitative properties of the recorded brain activity (single unit yield, spike amplitude and isolation distance) were compared between sites located at different positions of the silicon shank, focusing particularly on edge and center sites. Edge sites outperformed center sites: for all five probe types there was a significant difference in the signal power computed from the amplitude distributions, and edge sites recorded significantly more large amplitude samples both in the positive and negative range. Although the single unit yield was similar between site positions, the difference in spike amplitudes was noticeable in the range corresponding to high-amplitude spikes. Furthermore, the advantage of edge sites slightly decreased with decreasing shank width. Our results might aid the design of novel neural implants in enhancing their recording performance by identifying more efficient recording site placements.
Cellular automaton decoders for topological quantum codes with noisy measurements and beyond
Authors: Vasmer Michael , Browne Dan E. , Kubica Aleksander 
Published: January 2021

AbstractWe propose an error correction procedure based on a cellular automaton, the sweep rule, which is applicable to a broad range of codes beyond topological quantum codes. For simplicity, however, we focus on the three-dimensional toric code on the rhombic dodecahedral lattice with boundaries and prove that the resulting local decoder has a non-zero error threshold. We also numerically benchmark the performance of the decoder in the setting with measurement errors using various noise models. We find that this error correction procedure is remarkably robust against measurement errors and is also essentially insensitive to the details of the lattice and noise model. Our work constitutes a step towards finding simple and high-performance decoding strategies for a wide range of quantum low-density parity-check codes.
Evaluation of smartphone interactions on drivers’ brain function and vehicle control in an immersive simulated environment
Authors: Baker Joseph M. , Bruno Jennifer L. , Piccirilli Aaron , Gundran Andrew , Harbott Lene K. , Sirkin David. M. , Marzelli Matthew , Hosseini S. M. Hadi , Reiss Allan L. 
Published: January 2021

AbstractSmartphones and other modern technologies have introduced multiple new forms of distraction that color the modern driving experience. While many smartphone functions aim to improve driving by providing the driver with real-time navigation and traffic updates, others, such as texting, are not compatible with driving and are often the cause of accidents. Because both functions elicit driver attention, an outstanding question is the degree to which drivers’ naturalistic interactions with navigation and texting applications differ in regard to brain and behavioral indices of distracted driving. Here, we employed functional near-infrared spectroscopy to examine the cortical activity that occurs under parametrically increasing levels of smartphone distraction during naturalistic driving. Our results highlight a significant increase in bilateral prefrontal and parietal cortical activity that occurs in response to increasingly greater levels of smartphone distraction that, in turn, predicts changes in common indices of vehicle control.
Comparative analysis on the anti-inflammatory/immune effect of mesenchymal stem cell therapy for the treatment of pulmonary arterial hypertension
Authors: Oh Seyeon , Jang Albert Y. , Chae Sehyun , Choi Seungbum , Moon Jeongsik , Kim Minsu , Spiekerkoetter Edda , Zamanian Roham T. , Yang Phillip C. , Hwang Daehee , Byun Kyunghee , Chung Wook-Jin 
Published: January 2021

AbstractDespite the advancement of targeted therapy for pulmonary arterial hypertension (PAH), poor prognosis remains a reality. Mesenchymal stem cells (MSCs) are one of the most clinically feasible alternative treatment options. We compared the treatment effects of adipose tissue (AD)-, bone marrow (BD)-, and umbilical cord blood (UCB)-derived MSCs in the rat monocrotaline-induced pulmonary hypertension (PH) model. The greatest improvement in the right ventricular function was observed in the UCB-MSCs treated group. The UCB-MSCs treated group also exhibited the greatest improvement in terms of the largest decrease in the medial wall thickness, perivascular fibrosis, and vascular cell proliferation, as well as the lowest levels of recruitment of innate and adaptive immune cells and associated inflammatory cytokines. Gene expression profiling of lung tissue confirmed that the UCB-MSCs treated group had the most notably attenuated immune and inflammatory profiles. Network analysis further revealed that the UCB-MSCs group had the greatest therapeutic effect in terms of the normalization of all three classical PAH pathways. The intravenous injection of the UCB-MSCs, compared with those of other MSCs, showed superior therapeutic effects in the PH model for the (1) right ventricular function, (2) vascular remodeling, (3) immune/inflammatory profiles, and (4) classical PAH pathways.
Population difference gratings created on vibrational transitions by nonoverlapping subcycle THz pulses
Authors: Arkhipov Rostislav , Pakhomov Anton , Arkhipov Mikhail , Babushkin Ihar , Demircan Ayhan , Morgner Uwe , Rosanov Nikolay 
Published: January 2021

AbstractWe study theoretically a possibility of creation and ultrafast control (erasing, spatial frequency multiplication) of population density gratings in a multi-level resonant medium having a resonance transition frequency in the THz range. These gratings are produced by subcycle THz pulses coherently interacting with a nonlinear medium, without any need for pulses to overlap, thereby utilizing an indirect pulse interaction via an induced coherent polarization grating. High values of dipole moments of the transitions in the THz range facilitate low field strength of the needed THz excitation. Our results clearly show this possibility in multi-level resonant media. Our theoretical approach is based on an approximate analytical solution of time-dependent Schrödinger equation (TDSE) using perturbation theory. Remarkably, as we show here, quasi-unipolar subcycle pulses allow more efficient excitation of higher quantum levels, leading to gratings with a stronger modulation depth. Numerical simulations, performed for THz resonances of the$$H_20$$H20molecule using Bloch equations for density matrix elements, are in agreement with analytical results in the perturbative regime. In the strong-field non-perturbative regime, the spatial shape of the gratings becomes non-harmonic. A possibility of THz radiation control using such gratings is discussed. The predicted phenomena open novel avenues in THz spectroscopy of molecules with unipolar and quasi-unipolar THz light bursts and allow for better control of ultra-short THz pulses.