bluuebunny/crossref_metadata_2025 huggingface dataset:
Recognition and application of single sand-body in fluvial facies
Authors: He Yuhang
Published: November 2022

In the ultra-high water cut stage, the remaining oil of Lasaxing oilfields in Daqing placanticline, shows the distribution characteristics of highly dispersed and locally enriched, and the remaining geological reserves are still mainly distributed in fluvial reservoirs. In order to search and excavate the remaining oil of thick reservoir, the fine description technology of fluvial reservoir under the condition of dense well pattern was studied, and the recognition technology of meandering river and braided river single sand body was formed, which deepened the understanding degree of channel sand reservoir heterogeneity. The main controlling factors of remaining oil are defined, and the distribution mode of remaining oil is established, which can effectively guide the design of horizontal wells at the top of thick reservoir and the adjustment and exploitation of in-layer remaining oil tapping.
Climatic changes inferred from the chroma and magnetic susceptibility of aeolian deposits in the Central Shandong Mountains over the penultimate interglacial period
Authors: Zhao Qiuyue , Zhang Xinqi , Sun Yanping , Liu Xiuying , Ge Tianyan , Liu Ning , Tang Anrui , Zhou Rui
Published: November 2022

Loess-palaeosol sediments document the climatic changes and provide a good basis for palaeoclimate reconstruction. Palaeoclimatic changes of the holocene and the last interglacial period have been widely studied, but the penultimate interglacial period has been studied scarcely. The Dongheishan (DHS) section in the western of Shandong Province (China) preserves a loess-palaeosol sequence that includes the penultimate interglacial period. The annual average temperature and precipitation are retrieved by chroma and magnetic susceptibility (MS) to reconstruct the palaeoclimatic variations since the penultimate interglacial period. The results indicate that the lightness valley values and the redness and yellowness peaks correspond to the peak MS values, which can consistently reflect climate changes; redness and MS correlated well with the annual average temperature and annual precipitation, respectively. The annual average temperature is 14.4 °C based on redness in the the penultimate interglacial palaeosol, indicating that the palaeoclimate was warmer during the penultimate interglacial period than at present. The annual average precipitation is 349 mm derived from magnetic susceptibility, showing that the magnetic susceptibility should be cautious of the inversion of precipitation in the Central Shandong Mountains (CSM) region.
Fractal analysis on the effective heat conductivity of unsaturated soil
Authors: Su Shunyu , Li Wenlanting
Published: November 2022

Because of the complicated structure, the traditional Euclidean geometry is difficult to accurately describe the inner distribution of pore soil. According to the fractal laws of inner structure in porous media, a popular fractal capillary model was presented to study the three phase heat transfer in unsaturated soil. Considering the soil pore size and its tortuosity, by using the fractal method about pore size distribution and tortuosity to depict the scaling relationships, the aim of this paper is to derive the effective heat conductivity of unsaturated three phase soil. The predicting values show good agreement with the experimental values of literature while the saturation values of water are among 0.2 to 0.9. Major factors that influence the effective heat conductivity of unsaturated soil were analyzed. The heat transfer mechanism of unsaturated soil was also analyzed according to the results. The conclusions of this study could help promote the improvement of the design of buried pipe heat exchanger in unsaturated soil.
Characteristics of sedimentary system evolution and sequence stratigraphy boundary of Denglouku group in Xujiaweizi fault depression, Songliao Basin
Authors: Cui Kunning
Published: November 2022

In the previous studies on this area, the sequence division is relatively rough. This study has improved the precision, and the Denglouku formation is divided into 10 fourth-order sequences, with the thickness of each small layer of about 70-80m. The characteristics of each small sequence boundary are described, and three third-order, four fourth-order sequence flooding surfaces are found. The stratigraphic framework is established. From bottom to top, the base level of all strata shows decline-rise-decline, which means regression-transformation-regression.

The Denglouku 1st mainly includes lacustrine and fan delta, the sources of sediments from northeast, northwest, southwest and Southeast directions. In Denglouku 2nd and Denglouku 3rd, braided fluvial delta and intermittent lacustrine are dominant, which were controlled by the sedimentary systems from east, south, north, northeast, southwest, and the northwest. In Denglouku 4th, there is mainly braided fluvial, rarely are lacustrine and braided fluvial delta plain, the main source was from the northeast, and a small amount of source is from the west.
Delineating surface sediments physical properties in Ghudai Area, Kuwait
Authors: Al-Saleh Abeer , Ahmed Modi , Al-Dousari Noor , William Teena
Published: November 2022

There are three main challenges to establishing human settlements in Ghudai area at northern Kuwait Bay, namely; sand encroachment, water floods, and coastal erosion. Therefore, the particle size distribution percentage and statistical parameters in Ghudai surface sediments at the Kuwait Bay coast were determined and delineated in an attempt to display the depositional environment and its impact on the seedling growth of native plants. Particle sizes were assessed using a centrifugal particle analyzer and 373 samples representing the top 20 cm of surficial sediments were taken from the main geomorphological zones around Nitraria retusa and Lycium shawii nabkhas as dominant species in the study area, particle size percentages, and statistical size parameters were determined and delineated. The structural parameter distribution showed the dominance of medium sand sediments, as well as their environmental consequences revealing the unidirectional signature of fluvial flow from the Jal Al-Zur escarpment and wind transportation toward Kuwait Bay. Different discrimination maps of particle size parameters and other factors were plotted. The research shows that particle size parameters are highly vulnerable to slight changes in the pattern of sediment composition where sediments are deposited and reformed in disturbed environments.
Removal of Mn(II) from Acidic Wastewater on the Red Mud– Loess Mixture: Fixed–Bed Column Tests
Authors: Lu Yisi , Liu Xiaofeng , Xie Mingxing , Dong Xiaoqiang
Published: November 2022

In this study, the purification effect of red mud–loess mixture (RM–L) as a reactive medium in a permeable reactive barrier (PRB) for groundwater contaminated by acidic wastewater (AW) containing Mn(II) was explored considering removal capacity and pH value, and the safety of Mn(II) on RM–L after purification was evaluated. The breakthrough parameters of the Mn(II) were determined and the purifying performances of RM–L toward AW were evaluated by fixed-bed column tests at various initial concentrations of Mn(II), flow rates, and packing heights. The speciation of Mn(II) loaded on the RM–L was evaluated by the Tessier method. Results show the RM–L with a removal capacity of 17.30 mg·g−1 at 100 mg·L−1 initial concentration, 1 mL·min−1 flow rate and 7 cm packing height. The reduction in initial concentration and flow rate and the increase in packing height improve the total removal percentage of Mn(II) and the removal capacity of the RM–L. Moreover, the RM–L has a long-term effective acid buffer capacity for AW containing Mn(II), ensuring the pH values of effluent could be maintained at a neutral value. Furthermore, the Mn(II) could be loaded on the RM–L after the purification in stable forms that are dominated by the iron-manganese oxidate form.
Sterilization mechanism of helium/helium–oxygen atmospheric-pressure pulsed dielectric barrier discharge on membrane surface
Authors: CHEN Xingyu , LI Yuhan , LI Mengqi , XIONG Zilan
Published: November 2022

Pulsed dielectric barrier discharge (PDBD) exhibits several applications in different fields; however, the interaction of its components with substances remains a key issue. In this study, we employed experimental and numerical modeling to investigate the interactions between different PDBD components and substances in pure helium and a helium–oxygen mixture. A membrane comprising a Staphylococcus aureus strain was utilized as the treatment object to demonstrate the trace actions of the evolutions and distributions of certain components on the surface of the substance. The results revealed that the shapes and sizes of the discharging area and inhibition zone differed between groups. Under a pure helium condition, a discharge layer existed along the membrane surface, lying beside the main discharging channel within the electrode area. Further, an annulus inhibition zone was formed at the outer edge of the electrode in the pure helium group at 30 s and 1 min, and this zone extended to a solid circle at 2 min with a radius that was ∼50% larger than that of the electrode radius. Nevertheless, the discharging channel and inhibition zone in the helium–oxygen mixture were constrained inside the electrode area without forming any annulus. A 2D symmetrical model was developed with COMSOL to simulate the spatiotemporal distributions of different particles over the membrane surface, and the result demonstrated that the main components, which formed the annulus inhibition zone under the pure helium condition, contributed to the high concentration of the He+ annulus that was formed at the outer edge of the electrode. Moreover, O+ and

O

2

+

were the main components that killed the bacteria under the helium–oxygen mixture conditions. These results reveal that the homogenization treatment on a material surface via PDBD is closely related to the treatment time and working gas.
Efficient quantum state tracking in noisy environments
Authors: Rambach Markus , Youssry Akram , Tomamichel Marco , Romero Jacquiline
Published: November 2022

Quantum state tomography, which aims to find the best description of a quantum state—the density matrix, is an essential building block in quantum computation and communication. Standard techniques for state tomography are incapable of tracking changing states and often perform poorly in the presence of environmental noise. Although there are different approaches to solve these problems theoretically, experimental demonstrations have so far been sparse. Our approach, matrix-exponentiated gradient (MEG) tomography, is an online tomography method that allows for state tracking, updates the estimated density matrix dynamically from the very first measurements, is computationally efficient, and converges to a good estimate quickly even with very noisy data. The algorithm is controlled via a single parameter, its learning rate, which determines the performance and can be tailored in simulations to the individual experiment. We present an experimental implementation of MEG tomography on a qutrit system encoded in the transverse spatial mode of photons. We investigate the performance of our method on stationary and evolving states, as well as significant environmental noise, and find fidelities of around 95% in all cases.
Quantum scale estimation
Authors: Rubio Jesús
Published: November 2022

Quantum scale estimation, as introduced and explored here, establishes the most precise framework for the estimation of scale parameters that is allowed by the laws of quantum mechanics. This addresses an important gap in quantum metrology, since current practice focuses almost exclusively on the estimation of phase and location parameters. For given prior probability and quantum state, and using Bayesian principles, a rule to construct the optimal probability-operator measurement is provided. Furthermore, the corresponding minimum mean logarithmic error is identified. This is then generalised as to accommodate the simultaneous estimation of multiple scale parameters, and a procedure to classify practical measurements into optimal, almost-optimal or sub-optimal is highlighted. As a means of illustration, the new framework is exploited to generalise scale-invariant global thermometry, as well as to address the estimation of the lifetime of an atomic state. On a more conceptual note, the optimal strategy is employed to construct an observable for scale parameters, an approach which may serve as a template for a more systematic search of quantum observables. Quantum scale estimation thus opens a new line of enquire—the precise measurement of scale parameters such as temperatures and rates—within the quantum information sciences.
Towards a variational Jordan–Lee–Preskill quantum algorithm
Authors: Liu Junyu , Li Zimu , Zheng Han , Yuan Xiao , Sun Jinzhao
Published: November 2022

Rapid developments of quantum information technology show promising opportunities for simulating quantum field theory in near-term quantum devices. In this work, we formulate the theory of (time-dependent) variational quantum simulation of the

1
+
1

dimensional

λ

ϕ
4

quantum field theory including encoding, state preparation, and time evolution, with several numerical simulation results. These algorithms could be understood as near-term variational quantum circuit (quantum neural network) analogs of the Jordan–Lee–Preskill algorithm, the basic algorithm for simulating quantum field theory using universal quantum devices. Besides, we highlight the advantages of encoding with harmonic oscillator basis based on the Lehmann—Symanzik—Zimmermann reduction formula and several computational efficiency such as when implementing a bosonic version of the unitary coupled cluster ansatz to prepare initial states. We also discuss how to circumvent the ‘spectral crowding’ problem in the quantum field theory simulation and appraise our algorithm by both state and subspace fidelities.
Estimating the Long-Term Causal Effects of Attending Historically Black Colleges or Universities on Depressive Symptoms
Authors: Thyden Naomi Harada , McGuire Cydney , Slaughter-Acey Jaime , Widome Rachel , Warren John Robert , Osypuk Theresa L
Published: November 2022

Racism is embedded in society, and higher education is an important structure for patterning economic and health outcomes. Historically Black Colleges and Universities (HBCUs) were founded on antiracism while predominantly White institutions (PWIs) were often founded on white supremacy. This contrast provides an opportunity to study the association between structural racism and health among Black Americans. We used the National Longitudinal Study of Adolescent to Adult Health (Add Health) to estimate the long-term causal effect of attending an HBCU (vs. PWI) on depressive symptoms among Black students in the United States from 1994–2018. While we found no overall association with attending an HBCU (vs. PWI) on depressive symptoms, we found that this association varied by baseline mental health and region, and across time. For example, among those who attended high school outside of the South, HBCU attendance was protective against depressive symptoms 7 years later, and the association was strongest for those with higher baseline depressive symptoms. We recommend equitable state and federal funding for HBCUs, and that PWIs implement and evaluate antiracist policies to improve mental health of Black students.
Moving towards a taxonomy of cognitive impairments in epilepsy: application of latent profile analysis to 1178 patients with temporal lobe epilepsy
Authors: Reyes Anny , Hermann Bruce P , Busch Robyn M , Drane Daniel L , Barr William B , Hamberger Marla J , Roesch Scott C , McDonald Carrie R
Published: November 2022

In efforts to understand the cognitive heterogeneity within and across epilepsy syndromes, cognitive phenotyping has been proposed as a new taxonomy aimed at developing a harmonized approach to cognitive classification in epilepsy. Data- and clinically driven approaches have been previously used with variability in the phenotypes derived across studies. In our study, we utilize latent profile analysis to test several models of phenotypes in a large multicentre sample of patients with temporal lobe epilepsy and evaluate their demographic and clinical profiles. For the first time, we examine the added value of replacing missing data and examine factors that may be contributing to missingness. A sample of 1178 participants met the inclusion criteria for the study, which included a diagnosis of temporal lobe epilepsy and the availability of comprehensive neuropsychological data. Models with two to five classes were examined using latent profile analysis and the optimal model was selected based on fit indices, posterior probabilities and proportion of sample sizes. The models were also examined with imputed data to investigate the impact of missing data on model selection. Based on the fit indices, posterior probability and distinctiveness of the latent classes, a three-class solution was the optimal solution. This three-class solution comprised a group of patients with multidomain impairments, a group with impairments predominantly in language and a group with no impairments. Overall, the multidomain group demonstrated a worse clinical profile and comprised a greater proportion of patients with mesial temporal sclerosis, a longer disease duration and a higher number of anti-seizure medications. The four-class and five-class solutions demonstrated the lowest probabilities of a group membership. Analyses with imputed data demonstrated that the four-class solution was the optimal solution; however, there was a weak agreement between the missing and imputed data sets for the four-Class solutions (κ = 0.288, P < 0.001). This study represents the first to use latent profile analysis to test and compare multiple models of cognitive phenotypes in temporal lobe epilepsy and to determine the impact of missing data on model fit. We found that the three-phenotype model was the most meaningful based on several fit indices and produced phenotypes with unique demographic and clinical profiles. Our findings demonstrate that latent profile analysis is a rigorous method to identify phenotypes in large, heterogeneous epilepsy samples. Furthermore, this study highlights the importance of examining the impact of missing data in phenotyping methods. Our latent profile analysis-derived phenotypes can inform future studies aimed at identifying cognitive phenotypes in other neurological disorders.
Networks of cortical activity in infants with epilepsy
Authors: Auno Sami , Jonsson Henna , Linnankivi Tarja , Tokariev Anton , Vanhatalo Sampsa
Published: November 2022

Epilepsy in infancy links to a significant risk of neurodevelopmental delay, calling for a better understanding of its underlying mechanisms. Here, we studied cortical activity networks in infants with early-onset epilepsy to identify network properties that could pre-empt infants’ neurodevelopmental course. We studied high-density (64 channel) electroencephalogram during non-rapid eye movement (N2) sleep in n = 49 infants at 1 year of age after being diagnosed with epilepsy during their first year of life. We computed frequency-specific networks in the cortical source space for two intrinsic brain modes: amplitude–amplitude and phase–phase correlations. Cortical activity networks of all frequency bands and connectivity modes were compared between the syndrome groups as well as between the three categories of neurocognitive development. The group differences were studied at three spatial levels: global, regional, and individual connections. Cortical mechanisms related to infant epilepsy were further compared with physiological networks using an automatic spindle detection algorithm. Our results show that global connectivity does not significantly differ between epilepsy syndromes; however, it co-varies with neurocognitive development. The largest network differences were observed at the lowest (<1 Hz) and mid-range (10–15 Hz) frequency bands. An algorithmic removal of sleep spindles from the data partially reduced the mid-range frequency network’s strength. The centrocentral and frontocentral networks at the spindle frequencies were found to be strongest in infants with a persistent age-typical neurocognitive performance, while their low-frequency (< 1 Hz) networks were weaker for both amplitude-amplitude [P = 0.008, effect size = 0.61] and phase–phase correlations (P = 0.02, effect size = 0.54) at low (< 1 Hz). However, subjects with persistent mild neurocognitive delay from 1 to 2 years of age had higher amplitude–amplitude (P = 0.02, effect size = 0.73) and phase–phase (P = 0.06, effect size = 0.59) at low frequencies than those that deteriorated from mild to severely delayed from 1 to 2 years of age. Our findings suggest that cortical activity networks reflect the underlying clinical course of infants’ epilepsy, and measures of spectrally and spatially resolved networks might become useful in better understanding infantile epilepsy as a network disease.
Interplay of Atherogenic Particle Number and Particle Size and the Risk of Coronary Heart Disease
Authors: Pencina Karol M , Pencina Michael J , Lawler Patrick R , Engert James C , Dufresne Line , Ridker Paul M , Thanassoulis George , Mora Samia , Sniderman Allan D
Published: November 2022

Background

We examined the interplay of apolipoprotein B (apoB) and LDL particle size, approximated by the LDL-cholesterol (LDL-C)/apoB ratio, on the risk of new-onset coronary heart disease (CHD).

Methods

Participants without cardiovascular disease from the UK Biobank (UKB; n = 308 182), the Women’s Health Study (WHS; n = 26 204), and the Framingham Heart Study (FHS; n = 2839) were included. Multivariable Cox models were used to assess the relationship between apoB and LDL-C/apoB ratio and incidence of CHD (14 994 events). Our analyses were adjusted for age, sex (except WHS), HDL-cholesterol (HDL-C), systolic blood pressure, antihypertensive treatment, diabetes, and smoking.

Results

In all 3 studies, there was a strong positive correlation between apoB and LDL-C (correlation coefficients r = 0.80 or higher) and a weak inverse correlation of apoB with LDL-C/apoB ratio (−0.28 ≤ r ≤ −0.14). For all 3 cohorts, CHD risk was higher for higher levels of apoB. Upon multivariable adjustment, the association between apoB and new-onset CHD remained robust and statistically significant in all 3 cohorts with hazard ratios per 1 SD (95% CI): 1.24 (1.22–1.27), 1.33 (1.20–1.47), and 1.24 (1.09–1.42) for UKB, WHS, and FHS, respectively. However, the association between LDL-C/apoB and CHD was statistically significant only in the FHS cohort: 0.78 (0.64–0.94).

Conclusions

Our analysis confirms that apoB is a strong risk factor for CHD. However, given the null association in 2 of the 3 studies, we cannot confirm that cholesterol-depleted LDL particles are substantially more atherogenic than cholesterol-replete particles. These results lend further support to routine measurement of apoB in clinical care.
Estivation and Postestivation Development of Hemlock Woolly Adelgid (Adelges tsugae) (Hemiptera: Adelgidae) at Different Temperatures
Authors: Limbu Samita , Keena Melody A , Dietschler Nicholas , O’Connor Katharine , Whitmore Mark C
Published: November 2022

Hemlock woolly adelgid (Adelges tsugae) is the most important pest of hemlocks in the eastern United States, where it completes three generations a year. We investigated the impact of temperature (8, 12, 16, and 20°C) on the estivation and postaestivation stages of the A. tsugae sistens generation. Temperature significantly impacted development and survival of this generation. The highest mortality occurred at the coolest temperature (8°C). Adelges tsugae developed rapidly as the temperature increased and optimum temperatures for development ranged between 17 and 22°C for the different instars. The estimated lower temperature threshold was 0°C for second instar nymphs and 3 –5°C for the other instars and the preoviposition period. Estivating first-instar sistentes resumed development (as evidenced by segments becoming visible) after 40–100 d at the constant temperatures (fastest at 16°C) then required only 105 degree-days (DD) for 50% of the individuals to molt. Subsequent instars developed rapidly (another 470 DD total to reach adult), and oviposition began at ~623 DD from the time the first instars resumed development. This study provides valuable data required to develop an annual phenology model for A. tsugae which will assist in timing monitoring and control treatments.
Normative values of the aortic valve area and Doppler measurements using two-dimensional transthoracic echocardiography: results from the Multicentre World Alliance of Societies of Echocardiography Study
Authors: Cotella Juan I , Miyoshi Tatsuya , Mor-Avi Victor , Addetia Karima , Schreckenberg Marcus , Sun Deyu , Slivnick Jeremy A , Blankenhagen Michael , Hitschrich Niklas , Amuthan Vivekanandan , Citro Rodolfo , Daimon Masao , Gutiérrez-Fajardo Pedro , Kasliwal Ravi , Kirkpatrick James N , Monaghan Mark J , Muraru Denisa , Ogunyankin Kofo O , Park Seung Woo , Tude Rodrigues Ana Clara , Ronderos Ricardo , Sadeghpour Anita , Scalia Gregory , Takeuchi Masaaki , Tsang Wendy , Tucay Edwin S , Zhang Mei , Prado Aldo D , Asch Federico M , Lang Roberto M
Published: November 2022

Aims

Aortic valve area (AVA) used for echocardiographic assessment of aortic stenosis (AS) has been traditionally interpreted independently of sex, age and race. As differences in normal values might impact clinical decision-making, we aimed to establish sex-, age- and race-specific normative values for AVA and Doppler parameters using data from the World Alliance Societies of Echocardiography (WASE) Study.

Methods and results

Two-dimensional transthoracic echocardiographic studies were obtained from 1903 healthy adult subjects (48% women). Measurements of the left ventricular outflow tract (LVOT) diameter and Doppler parameters, including AV and LVOT velocity time integrals (VTIs), AV mean pressure gradient, peak velocity, were obtained according to ASE/EACVI guidelines. AVA was calculated using the continuity equation. Compared with men, women had smaller LVOT diameters and AVA values, and higher AV peak velocities and mean gradients (all P < 0.05). LVOT and AV VTI were significantly higher in women (P < 0.05), and both parameters increased with age in both sexes. AVA differences persisted after indexing to body surface area. According to the current diagnostic criteria, 13.5% of women would have been considered to have mild AS and 1.4% moderate AS. LVOT diameter and AVA were lower in older subjects, both men and women, and were lower in Asians, compared with whites and blacks.

Conclusion

WASE data provide clinically relevant information about significant differences in normal AVA and Doppler parameters according to sex, age, and race. The implementation of this information into clinical practice should involve development of specific normative values for each ethnic group using standardized methodology.
Welfare Cuts and Crime: Evidence from the New Poor Law
Authors: Melander Eric , Miotto Martina
Published: November 2022

The New Poor Law reform of 1834 induced dramatic and heterogeneous reductions in welfare spending across English and Welsh counties. Using the reform in a difference-in-differences instrumental variables strategy, we document a robust negative relationship between the generosity of welfare provision and criminal activity. Results are driven by non-violent property crimes and are stronger during months of seasonal agricultural unemployment, highlighting the particularly criminogenic combination of welfare cuts and precarious work opportunities for the economically vulnerable.
Violin-making in Rome, 1700−1830: new archival investigations
Authors: Barbieri Patrizio
Published: November 2022

In the 16th and 17th centuries, Roman production in the lutherie sector focused almost exclusively on plucked-string instruments: in the numerous workshop inventories that have come down to us, the various members of the viola family are very rare indeed, while violins are almost entirely absent. Again in Rome, the profession of violin-maker (‘violinaro’) starts to appear only in the second quarter of the 18th century; unlike the situation with the luthiers of the two previous centuries, only one workshop inventory has previously been described from this type of maker: that of the ‘violinaro’ Crescenzio Ugar (1791), which unfortunately provides very little information about the maker’s effective production.

This article aims to help to fill the gap, which is all the more serious since it concerns a class of instruments that (unlike those of the plucked-string type) was the most valued from the 18th century onwards—not only from a musical point of view, but also from a purely economic perspective. I refer in particular to three previously unpublished inventories of the stock of well-known violinari operating in Rome: Francesco Emiliani (1736), Giulio Cesare Gigli (1794) and Giovanni Maria Valenzano (1826). To these we may add Magno Longo (1704), one of just two guitar-makers (‘chitarrari’) of German origin, from whose workshop we also find documentation concerning the production of violins. I also present a review of the instruments played by several Roman violinists during the 18th and 19th centuries.
Impact of Lactobacillus-originated metabolites on enterohemorrhagic E. coli in rumen fluid
Authors: Aditya Arpita , Rahaman Shaik O , Biswas Debabrata
Published: November 2022

Rumen is one of the richest microbial ecosystems naturally harboring many zoonotic pathogens. Controlling the colonization of cattle originated zoonotic pathogens in rumen, particularly enterohemorrhagic Escherichia coli (EHEC), is critical in reducing foodborne enteric diseases in humans. In this study, we aimed to inhibit the growth of EHEC in a simulated rumen system with collected rumen fluids (RFs) using live probiotics, synbiotics, and their metabolites. EHEC inoculated RF was treated with live wild type Lactobacillus casei (LCwt), LCwt with 0.5% peanut flour (LCwt+PF), an engineered LC capable of overexpressing linoleate isomerase (LCCLA), and their metabolites collected in cell-free culture supernatants (CFCSwt, CFCSwt+PF, and CFCSCLA) at various time points. A growth stimulatory effect toward Lactobacillus spp. was exerted by all CFCS, while the EHEC was suppressed. Among other treatments only LCwt+PF reduced EHEC by 2.68 logs after 72 h. This observation was also supported by metataxonomic analysis. A reduction in Bacteroidetes and Proteobacteria while increase in Firmicutes was observed at 48 h by the presence of CFCSs as compared to the control. Our observation implies probiotic-originated metabolites modulate rumen microbiota positively which can be deployed to control the transmission of cattle-borne pathogens specifically EHEC.
A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)
Authors: Brůna Tomáš , Aryal Rishi , Dudchenko Olga , Sargent Daniel James , Mead Daniel , Buti Matteo , Cavallini Andrea , Hytönen Timo , Andrés Javier , Pham Melanie , Weisz David , Mascagni Flavia , Usai Gabriele , Natali Lucia , Bassil Nahla , Fernandez Gina E , Lomsadze Alexandre , Armour Mitchell , Olukolu Bode , Poorten Thomas , Britton Caitlin , Davik Jahn , Ashrafi Hamid , Aiden Erez Lieberman , Borodovsky Mark , Worthington Margaret
Published: November 2022

Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession “Hillquist” (R. argutus). “Hillquist” is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The “Hillquist” assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the “Hillquist” genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.
Persistent Müllerian duct syndrome associated with genetic defects in the regulatory subunit of myosin phosphatase
Authors: Picard Jean-Yves , Morin Gilles , Devouassoux-Shisheboran Mojgan , Van der Smagt Jasper , Klosowski Serge , Pienkowski Catherine , Pierre-Renoult Peggy , Masson Cécile , Bole Christine , Josso Nathalie
Published: November 2022

STUDY QUESTION

Can mutations of genes other than AMH or AMHR2, namely PPP1R12A coding myosin phosphatase, lead to persistent Müllerian duct syndrome (PMDS)?

SUMMARY ANSWER

The detection of PPP1R12A truncation mutations in five cases of PMDS suggests that myosin phosphatase is involved in Müllerian regression, independently of the anti-Müllerian hormone (AMH) signaling cascade.

WHAT IS KNOWN ALREADY

Mutations of AMH and AMHR2 are detectable in an overwhelming majority of PMDS patients but in 10% of cases, both genes are apparently normal, suggesting that other genes may be involved.

STUDY DESIGN, SIZE, DURATION

DNA samples from 39 PMDS patients collected from 1990 to present, in which Sanger sequencing had failed to detect biallelic AMH or AMHR2 mutations, were screened by massive parallel sequencing.

PARTICIPANTS/MATERIALS, SETTING, METHODS

To rule out the possibility that AMH or AMHR2 mutations could have been missed, all DNA samples of good quality were analyzed by targeted next-generation sequencing. Twenty-four samples in which the absence of AMH or AMHR2 biallelic mutations was confirmed were subjected to whole-exome sequencing with the aim of detecting variants of other genes potentially involved in PMDS.

MAIN RESULTS AND THE ROLE OF CHANCE

Five patients out of 24 (21%) harbored deleterious truncation mutations of PP1R12A, the gene coding for the regulatory subunit of myosin phosphatase, were detected. In addition to PMDS, three of these patients presented with ileal and one with esophageal atresia. The congenital abnormalities associated with PMDS in our patients are consistent with those described in the literature for PPP1R12A variants and have never been described in cases of AMH or AMHR2 mutations. The role of chance is therefore extremely unlikely.

LIMITATIONS, REASONS FOR CAUTION

The main limitation of the study is the lack of experimental validation of the role of PPP1R12A in Müllerian regression. Only circumstantial evidence is available, myosin phosphatase is required for cell mobility, which plays a major role in Müllerian regression. Alternatively, PPP1R12A mutations could affect the AMH transduction pathway.

WIDER IMPLICATIONS OF THE FINDINGS

The study supports the conclusion that failure of Müllerian regression in males is not necessarily associated with a defect in AMH signaling. Extending the scope of molecular analysis should shed light upon the mechanism of the initial steps of male sex differentiation.

STUDY FUNDING/COMPETING INTEREST(S)

The study was funded by la Fondation Maladies Rares, GenOmics 2021_0404 and la Fondation pour la Recherche Médicale, grant EQU201903007868. The authors report no conflict of interest.

TRIAL REGISTRATION NUMBER

N/A.
On a random entanglement problem
Authors: Bonner Gage , Thiffeault Jean-Luc , Valkó Benedek
Published: November 2022

We study a model for the entanglement of a two-dimensional reflecting Brownian motion in a bounded region divided into two halves by a wall with three or more small windows. We map the Brownian motion into a Markov Chain on the fundamental groupoid of the region. We quantify entanglement of the path with the length of the appropriate element in this groupoid. Our main results are a law of large numbers and a central limit theorem for this quantity. The constants appearing in the limit theorems are expressed in terms of a coupled system of quadratic equations.
Ileal and total tract digestibility of energy and nutrients in pig diets supplemented with a novel consensus bacterial 6-phytase variant
Authors: Espinosa Charmaine D , Torres Leidy J , Velayudhan Deepak E , Dersjant-Li Yueming , Stein Hans H
Published: November 2022

An experiment was conducted to test the hypothesis that increasing levels of a novel phytase increases the apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of nutrients in diets fed to young pigs. A negative control (NC) diet based on corn, soybean meal, and canola meal that contained approximately 0.83% phytate (i.e., 0.23% phytate-bound P) was formulated to be deficient in Ca, P, and standardized ileal digestible amino acids (AA). Five additional diets were formulated by adding 250, 500, 1,000, 2,000, or 4,000 phytase units/kg of the novel phytase to the NC diets. Eighteen ileal-cannulated pigs (17.81 ± 1.71 kg) were allotted to a 6 × 3 incomplete Latin square design with six diets and three 11-day periods. There were three pigs per diet in each period; therefore, there were nine replicate pigs per diet. The initial 5 d of each period was considered an adaptation period to the diet. For each period, fecal samples were collected via anal stimulation on days 6, 7, 8, and 9, whereas ileal digesta were collected on days 10 and 11 using standard procedures. Results indicated that the AID of crude protein, indispensable AA, and dispensable AA was increased (quadratic, P < 0.05) as the concentration of microbial phytase increased in the diets. Dietary inclusion of the novel phytase at 1,000 or 2,000 FTU/kg increased the AID of total AA from 73.7% to 79.8%. Increasing levels of microbial phytase increased (quadratic, P < 0.05) the AID of dry matter and minerals (i.e., Ca, P, K, Mg, Cu) in the diets. Likewise, a linear increase (P < 0.05) in the AID of ash and Na was observed as the inclusion level of phytase increased in the diets. Increasing levels of microbial phytase increased (linear, P < 0.01) the AID of gross energy (GE) and starch in the diets. A quadratic (P < 0.05) increase in the ATTD of ash, Ca, P, K, and Cu in experimental diets was observed as the concentration of microbial phytase increased in the diets. The ATTD of Mg and GE also increased (linear; P < 0.05) as concentration of dietary phytase increased. In conclusion, the novel microbial phytase used in this experiment was effective in increasing the AID of dry matter, GE, starch, minerals, and AA, as well as the ATTD of gross energy and minerals in diets formulated to be deficient in Ca, P, and AA.
Exploring differentially expressed genes in hypothalamic, pars tuberalis and pineal gland transcriptomes in different sexual behavior phenotypes in rams using RNA-Seq
Authors: Lakhssassi Kenza , Sarto María Pilar , Marín Belén , Lahoz Belén , Folch José , Alabart José Luis , Serrano Malena , Calvo Jorge Hugo
Published: November 2022

Reproductive seasonality is a limiting factor in sheep production. Sexual behavior is a key element in reproductive efficiency, and this function is regulated by the hypothalamus-pituitary-gonadal (HPG) axis. To understand the mechanisms of sexual behavior, transcriptomic sequencing technology was used to identify differentially expressed genes (DEGs) in the hypothalamus (HT), pars tuberalis (PT) and pineal gland (PG) in Rasa Aragonesa rams with different sexual behavior. Bioinformatics analysis of the 16,401 identified genes by RNA-Seq revealed 103 and 12 DEGs in the HT and the PG, respectively, at a false discovery rate (FDR) of 5% with an absolute value of expression ≥ 1 (log2FC). However, no DEGs were found in the PT. Functional annotation and pathway enrichment analysis showed that DEGs of HT were enriched mainly in neuroactive ligand-receptor interactions and signaling pathways, including notable candidate genes such as MTNR1A, CHRNA2, FSHB, LHB, GNRHR, AVP, PRL, PDYN, CGA, GABRD, and TSHB, which play a crucial role in sexual behavior. The GnRH and cAMP signaling pathways were also highlighted. In addition, gene set enrichment analysis (GSEA) identified potential pathways, dominated mainly by biological process category, that could be responsible for the differences in sexual behavior observed in rams. The intracellular protein transport and pattern specification process were enriched within the PT and the transcription factor binding and protein ubiquitination pathways for the PG. Thus, these pathways together may play an important role in the regulation of the sexual behavior in Rasa Aragonesa rams through the hypothalamic-pituitary-gonadal axis. The validation of 5 DEGs using reverse transcription quantitative polymerase chain reaction (RT-qPCR) showed expression patterns like the found with RNA-Seq. Overall, these results contribute to understanding the genomic basis of sexual behavior in rams. Our study demonstrates that multiple networks and pathways orchestrate sexual behavior in sheep.
Darknet imaginaries in Internet memes: the discursive malleability of the cultural status of digital technologies
Authors: Siuda Piotr , Nowak Jakub , Gehl Robert W
Published: November 2022

Dominant discourses on the darknet present it either as a dangerous space with flourishing crime or a place for civic action and political activism. However, these depictions have been challenged in online popular culture, particularly in memes. By utilizing the concepts of double articulation of media and cultural imaginaries, this article reveals how memes shape popular definitions of darknet. Our qualitative, social semiotic content analysis of 505 memes reveals an ambiguous and complex vision of the darknet that both supports and demystifies the mainstream imagery. We introduce the concept of discursive malleability of niche technologies to describe how cultural practices reshape technologies, especially those with small userbases. Additionally, we present a “representational map of the darknet” and indicate how this contributes to social understanding of digital technologies more generally, and, not least why the analyzed memes may be read as lens exposing contradictory notions and policies regarding digital technologies nowadays.
Neuropathology of classic myotonic dystrophy type 1 is characterized by both early initiation of primary age-related tauopathy of the hippocampus and unique 3-repeat tauopathy of the brainstem
Authors: Hamasaki Hideomi , Maeda Norihisa , Sasagasako Naokazu , Honda Hiroyuki , Shijo Masahiro , Mori Shin-Ichiro , Yagita Kaoru , Arahata Hajime , Iwaki Toru
Published: November 2022

Myotonic dystrophy type 1 (DM1) is an inherited autosomal-dominant condition that induces altered splicing of transcripts, including MAPT, leading to a distinctive abnormal deposition of tau protein in the CNS. We characterized the tau isoforms of abnormal depositions in the brains of 4 patients with classic DM1 by immunohistochemistry using isoform-specific antibodies. All patients, including those of presenile age, showed numerous neurofibrillary tangles (NFTs) of both 3-repeat and 4-repeat tau in the limbic area and mild involvement in the cerebral cortex. Amyloid-β deposition was only seen in 1 senile case while cortical tauopathy in all other cases was consistent with primary age-related tauopathy (PART). In the putamen and globus pallidus, only a few tau deposits were observed. Tau deposits in the brainstem frequently showed a DM1-specific pattern with 3-repeat tau dominant NFTs. Additionally, tau-positive astrocytes morphologically similar to tufted astrocytes and astrocytic plaques were occasionally observed in the brainstem; however, they were predominantly composed of 3-repeat tau. Thus, the classic DM1 showed both early onset of PART-like pathology in the limbic areas as a progeroid syndrome of DM1 and an abnormal splicing event in the brainstem leading to 3-repeat tau dominant accumulation with both neuronal and astrocytic involvement.
Syncope after a long-haul flight revealing multiple embolic events: the management strategy dilemma
Authors: Raye Eugénie , Martineau Laurence , Adnet Frédéric , Petrovic Tomislav , Lapostolle Frédéric
Published: November 2022

Air travel-related pulmonary embolism is rarely associated with other embolic complications, such as stroke, ST-segment elevation acute coronary syndrome and other systemic events we presented in our case report. In such a situation, physicians will face several dilemmas. We propose strategic avenues to answer this.
Rapid spread of a new West Nile virus lineage 1 associated with increased risk of neuroinvasive disease during a large outbreak in Italy in 2022
Authors: Barzon Luisa , Pacenti Monia , Montarsi Fabrizio , Fornasiero Diletta , Gobbo Federica , Quaranta Erika , Monne Isabella , Fusaro Alice , Volpe Andrea , Sinigaglia Alessandro , Riccetti Silvia , Dal Molin Emanuela , Satto Sorsha , Lisi Vittoria , Gobbi Federico , Galante Silvia , Feltrin Giuseppe , Valeriano Valerio , Favero Laura , Russo Francesca , Mazzucato Matteo , Bortolami Alessio , Mulatti Paolo , Terregino Calogero , Capelli Gioia
Published: November 2022

Background

A new strain of West Nile virus lineage 1 (WNV-1) emerged in the Veneto Region, northern Italy, in 2021, 8 years after the last WNV-1 outbreak in Italy. The virus, which co-circulates with West Nile virus lineage 2 (WNV-2), has become endemic in the region, where, in 2022, most human cases of neuroinvasive disease (WNND) reported in Europe have occurred.

Methods

Comparative analysis of the epidemiology and clinical presentation of WNV-1 and WNV-2 infection in humans, as well as the temporal and geographic distribution of WNV-1 and WNV-2 among wild birds and Culex pipiens mosquitoes in Veneto, from 16 May to 21 August 2022, to determine if the high number of WNND cases was associated with WNV-1.

Results

222 human cases of WNV infection were confirmed by molecular testing, including 103 with West Nile fever (WNF) and 119 with WNND. The WNV lineage was determined in 201 (90.5%) cases, comprising 138 WNV-1 and 63 WNV-2 infections. In addition, 35 blood donors tested positive, including 30 in whom WNV lineage was determined (13 WNV-1 and 17 WNV-2). Comparative analysis of the distribution of WNV-1 and WNV-2 infections among WNND cases, WNF cases and WNV-positive blood donors showed that WNND patients were more likely to have WNV-1 infection than blood donors (odds ratio 3.44; 95% confidence interval: 1.54–8.24; P = 0.0043). As observed in humans, in wild birds, WNV-1 had a higher infection rate (IR) and showed a more rapid expansion than WNV-2. At variance, the distribution of the two lineages was more even in mosquitoes, but with a trend of rapid increase of WNV-1 IR over WNV-2.

Conclusions

Comparative analysis of WNV-1 vs WNV-2 infection in humans, wild birds and mosquitos showed a rapid expansion of WNV-1 and suggested that WNV-1-infected patients might have an increased risk to develop severe disease.