bluuebunny/crossref_metadata_2025 huggingface dataset:
Revisiting the top-quark pair production at future e
+
e
− colliders*
Authors: Ma 马 Jin 进 , Wang 王 Sheng-Quan 声权 , Sun 孙 Ting 婷 , Shen 申 Jian-Ming 建明 , Wu 吴 Xing-Gang 兴刚
Published: January 2024

In this study, we reanalyze the top-quark pair production at next-to-next-to-leading order (NNLO) in quantum chromodynamics (QCD) at future

colliders using the Principle of Maximum Conformality (PMC) method. The PMC renormalization scales in

are determined by absorbing the non-conformal β terms by recursively using the Renormalization Group Equation (RGE). Unlike the conventional scale-setting method of fixing the scale at the center-of-mass energy

, the determined PMC scale

is far smaller than the

and increases with the

, yielding the correct physical behavior for the top-quark pair production process. Moreover, the convergence of the pQCD series for the top-quark pair production is greatly improved owing to the elimination of the renormalon divergence. For a typical collision energy of

GeV, the PMC scale is

GeV; the QCD correction factor K for conventional results is

, where the first error is caused by varying the scale

and the second error is from the top-quark mass

GeV. After applying the PMC, the renormalization scale uncertainty is eliminated, and the QCD correction factor K is improved to

, where the error is from the top-quark mass

GeV. The PMC improved predictions for the top-quark pair production are helpful for detailed studies of the properties of the top-quark at future

colliders.
The effects of social distancing markers on single-file pedestrian movement during the pandemic
Authors: Lu Tuantuan , Zhu Pengfei
Published: January 2024

Social distancing markers placed on the floor are a commonly used measure by city authorities to remind pedestrians to keep a safe distance during the pandemic. However, little is known about the effects of social distancing markers on pedestrian dynamics. In this paper, we conducted a series of single-file experiments with and without social distancing markers under a prescribed social distance of 1 m. By comparing the trajectories with and without social distancing markers, the two-sided effects of social distancing markers are revealed. Pedestrians have significantly fewer social distance violations and less exposure time with the help of social distancing markers, which can decrease the total infection risk. However, pedestrians under the measure of social distancing markers need longer delay times for velocity-matching behavior; also, lower velocity and specific flow are observed at densities greater than 0.6 m−1, which will increase the queue length. Stepping behavior is further analyzed to reveal the impact mechanism behind the reduction in velocity and specific flow. It is found that pedestrians’ step length is sensitive to social distancing markers, and pedestrians tend to shorten their step length rather than step frequency more rapidly when the markers are implemented. These evidence-based results provide interesting insights for crowd management, and help to develop pedestrian simulation models in preparation for future outbreaks and pandemics.
System for the fast readout and tests of pixel IC operating in single photon counting mode using PCIe-based FPGA
Authors: Skrzypiec P. , Gryboś P. , Szczygieł R.
Published: January 2024

Hybrid Pixel Detectors (HPDs) have become popular in particle and photon detection
techniques in recent years. This type of devices consists of two parts: a pixelated sensor (based
on Si, Ge, GaAs, CZT, etc.), and a readout Integrated Circuit (IC), which usually contains
thousands of pixels and millions of transistors. ICs suffer from the inaccuracies of
manufacturing processes, therefore HPDs have to be thoroughly tested before the sensor
bump-bonding process.

This paper presents a highly efficient system for the automated testing of pixelated HPDs. The presented solution is based on the Intel Arria 10 GX Field
Programmable Gate Array (FPGA) development kit and a Linux-powered Personal Computer (PC),
connected via Peripheral Component Interconnect Express (PCIe) 8x Gen. 3 interface. The proposed
system has been built of well-thought-out modules connected through the set of precisely defined
interconnects. This approach enabled the development of an architecture that may be easily
implemented in both PCIe-based systems and
System-on-Chip devices, such as Intel Agilex SoC. The presented system has been tested with
both a manufactured IC and a model implemented in the FPGA.
Ultra-low work function of caesiated surfaces and impact of selected gas species
Authors: Heiler A. , Friedl R. , Fantz U.
Published: January 2024

Modern high-power negative hydrogen ion sources rely predominantly on the surface
production of negative hydrogen ions. Hence, low work function converter surfaces are mandatory,
for which the alkali metal Cs is commonly evaporated into the ion source to lower the work
function of refractory metals by surface adsorption. To study the work function behaviour upon
caesiation under the typically given non-ultra-high vacuum conditions, investigations are
performed at a dedicated laboratory experiment. In a vacuum environment dominated by water vapour,
the work function evolution is found to be dependent on the flux ratio of Cs to H2O onto the
surface. For sufficiently high flux ratios, ultra-low work functions in the range of
1.25±0.10 eV are generated with excellent reproducibility. In the absence of Cs evaporation,
the work function gradually increases under the influence of the residual gases, and re-caesiation
processes lead to lower quantum efficiencies and higher work functions of typically
1.9–2.1 eV. While the addition of hydrogen and deuterium gas at several Pa as well as the
leakage of inert gases (argon and nitrogen) into the vacuum system have a negligible influence on
the caesiation process, small amounts of oxygen with partial pressures of
∼10-2–10-1 Pa lead to an instant reduction of the Cs density in the gas phase by
several orders of magnitude and to an increase in the work function of the order of 1 eV. After
the oxygen exposure is terminated, however, the Cs density and work function fully recover within
several minutes.
Electron transfer efficiency in liquid xenon across THGEM holes
Authors: Martínez-Lema G. , Roy A. , Breskin A. , Arazi L.
Published: January 2024

Dual-phase liquid-xenon time projection chambers (LXe TPCs)
deploying a few tonnes of liquid are presently leading the search
for WIMP dark matter. Scaling these detectors to 10-fold larger
fiducial masses, while improving their sensitivity to low-mass WIMPs
presents difficult challenges in detector design. Several groups are
considering a departure from current schemes, towards either
single-phase liquid-only TPCs, or dual-phase detectors where the
electroluminescence region consists of patterned electrodes. Here,
we discuss the possible use of Thick Gaseous Electron Multipliers
(THGEMs) coated with a VUV photocathode and immersed in LXe as a
building block in such designs. We focus on the transfer
efficiencies of ionization electrons and photoelectrons emitted from
the photocathode through the electrode holes and show experimentally
that efficiencies approaching 100% can be achieved with realistic
voltage settings. The observed voltage dependence of the transfer
efficiencies is consistent with electron transport simulations once
diffusion and charging-up effects are included.
Increasing influence of evapotranspiration on prolonged water storage recovery in Germany
Authors: Boeing Friedrich , Wagener Thorsten , Marx Andreas , Rakovec Oldrich , Kumar Rohini , Samaniego Luis , Attinger Sabine
Published: January 2024

Central Europe, including Germany, has faced exceptional multi-year terrestrial water storage (TWS) deficits since 2018, negatively impacting various sectors such as forestry, energy production, and drinking water supply. Currently, the understanding of the recovery dynamics behind such extreme events is limited, which hampers accurate water management decisions. We used a simulation of the mesoscale hydrological model (mHM) over the last 257 years (1766–2022) to provide the first long-term perspective on the dynamics of the TWS deficit recovery in Germany. The results show that severe TWS deficits surpassing a peak deficit of −42 mm (−15 km3) exhibit large variability in recovery times (3–31 months). The 2018–2021 TWS deficit period was unprecedented in terms of recovery time (31 months), mean intensity and the associated negative 30-year TWS trend. In recent decades, we identified increased evapotranspiration (E) fluxes that have impacted TWS dynamics in Germany. Increased E flux anomalies contributed to prolonged TWS recovery, given that the TWS deficit did not quickly recover through above-average precipitation (P). An extreme TWS deficit similar to that in 2018 was recovered by above-average P within three months in the winter of 1947–1948. Our research contributes to an improved understanding of the dynamics and drivers of TWS deficit recovery.
Assessment of Soil Degradation for Biomass Production in Tanjungpinang, Indonesia
Authors: Danardono  , Taryono  , Ridwan Saiful
Published: January 2024

Land management, especially land that is not in accordance with the rules can cause damage/change in soil properties which in turn impacts the disruption of biomass production. The lack of available data regarding soil degradation, especially in Tanjungpinang City, has resulted in less than optimal supervision and control over land management. Mapping the condition of soil degradation is necessary to exercise control over land management. The purpose of this research is to assess soil degradation in Tanjungpinang City, Riau Archipelago for biomass production. Soil degradation can be modeled by scoring and overlaying four parameters, namely land use, slope, soil type, and rainfall, producing a tentative map of potential soil degradation. Next, a tentative map of soil degradation is corrected using a field survey. Field surveys are used to measure the standard criteria for soil degradation according to Government Regulation No. 150 of 2000. The results show that the criteria for soil degradation in Tanjungpinang City are light damage and moderate damage. The criteria for moderate damage have the largest area spread over Dompak Sub-District, Batu Sembilan, Melayu City Plate, Bukit Cermin, West Tanjungpinang, East Tanjungpinang, Kampung Baru, and Tanjung Ayun Sakti. The main limiting factors that limit land use in Tanjungpinang City are permeability, surface rocks, and redox.
Spatial-Temporal Analysis of Urban Heat Island Phenomenon 2014-2021 in Cianjur District
Authors: Inayah K , Wibowo Adi
Published: January 2024

Cianjur District is one of the areas in Cianjur Regency, West Java, Indonesia, which is the center of community activities. These community activities allow the Cianjur District area to experience massive urbanization and development to meet the growing demand for land increase. This research aims to analyze the spatial distribution of urban phenomena Heat Island (UHI) in Cianjur District and the association between LST and NDVI in Cianjur District. This research uses Landsat 8 data to analyze UHI with LST values. Correlation analysis was also performed to see the association between LST and vegetation density. Based on LST data processing, the temperature in 2014 and 2021 showed that 2014 10 Villages had a surface temperature above 30°C, so they experienced the UHI Phenomenon. The village comprises Bojongherang, Muka, Pamoyanan, Solokpandan, Sayang, Sawahgede, Mekarsari, Limbangansari, Nagrak, and Sukamaju. In 2021, the UHI phenomenon will expand to all villages. LST in Cianjur Regency has a robust negative correlation with NDVI, both in 2014 and 2021. So, the more dense vegetation, the lower is LST, and vice versa.
Study of Social Vulnerability in the Land Sector in Kutai Kartanegara
Authors: Setyasih Iya’ , Anwar Yaskinul , Wijaya Akhmad , Nanang Martinus , Gugus Perdana M , Dita Samsudin Rizka
Published: January 2024

Social vulnerability in the land sector is a problem that is not directly visible, which is caused by conflict, both between individuals and with the government or the private sector. This vulnerability will be more difficult to resolve, especially with the absence of land ownership status in several villages, including Tanjung Harapan and Sanggulan Villages. The purpose of this research is to comprehensively examine the social risks that can be experienced by vulnerable groups. This study uses qualitative and quantitative approaches to assess the level of social vulnerability. The level of vulnerability is seen based on the Household Vulnerability Index (HVI) approach. Data collection was carried out through questionnaires and interviews with 50 respondents in the villages of Tanjung Harapan and Sanggulan. The social vulnerability in the two villages is at level III or ELH, which means it includes chronic social vulnerability and needs special treatment. The vulnerability of this community is influenced by factors of knowledge and analysis of social, economic, physical, and environmental factors that make the community more vulnerable. In order to reduce high social risks, there needs to be certainty and protection for the community, especially farmers who own land with an area of less than 0.5 ha, women and the poor. So that it needs various efforts through policies and implementation methodologies for addressing land social vulnerabilities.
Rab11 regulates autophagy at dendritic spines in an mTOR- and NMDA-dependent manner
Authors: Janusz-Kaminska Aleksandra , Brzozowska Agnieszka , Tempes Aleksandra , Urbanska Malgorzata , Blazejczyk Magdalena , Miłek Jacek , Kuzniewska Bozena , Zeng Juan , Wesławski Jan , Kisielewska Katarzyna , Bassell Gary J. , Jaworski Jacek
Published: January 2024

Synaptic plasticity is a process that shapes neuronal connections during neurodevelopment and learning and memory. Autophagy is a mechanism that allows the cell to degrade its unnecessary or dysfunctional components. Autophagosomes appear at dendritic spines in response to plasticity-inducing stimuli. Autophagy defects contribute to altered dendritic spine development, autistic-like behavior in mice, and neurological disease. While several studies have explored the involvement of autophagy in synaptic plasticity, the initial steps of the emergence of autophagosomes at the postsynapse remain unknown. Here, we demonstrate a postsynaptic association of autophagy-related protein 9A (Atg9A), known to be involved in the early stages of autophagosome formation, with Rab11, a small GTPase that regulates endosomal trafficking. Rab11 activity was necessary to maintain Atg9A-positive structures at dendritic spines. Inhibition of mTOR increased Rab11 and Atg9A interaction and increased the emergence of LC3 positive vesicles, an autophagosome membrane-associated protein marker, in dendritic spines when coupled to NMDA receptor stimulation. Dendritic spines with newly formed LC3+ vesicles were more resistant to NMDA-induced morphologic change. Rab11 DN overexpression suppressed appearance of LC3+ vesicles. Collectively, these results suggest that initiation of autophagy in dendritic spines depends on neuronal activity and Rab11a-dependent Atg9A interaction that is regulated by mTOR activity.
Association of Variability and Hypertensive Loads in 24-h Blood Pressure With Mortality and Cardiovascular Risk
Authors: Melgarejo Jesus D , Patil Dhrumil , Mena Luis J , Vatcheva Kristina P , Garcia Jose A , Satizabal Claudia L , Chavez Carlos A , Pirela Rosa V , Silva Egle , Calmon Gustavo , Lee Joseph H , Terwilliger Joseph D , Seshadri Sudha , Maestre Gladys E
Published: January 2024

BACKGROUND

Evidence shows that high 24-h blood pressure (BP) variability increases cardiovascular risk. We investigated whether 24-h BP variability relates to mortality and cardiovascular risk due to inherent variability and/or hypertensive loads in 24-h BP.

METHODS

A total of 1,050 participants from the Maracaibo Aging Study (mean age, 66 years; women, 67.2%) underwent 24-h ambulatory BP monitoring and were followed between 2001 and 2016. To evaluate inherent BP variability, we used average real variability (ARV) as it captures variability among consecutive BP readings. 24-h systolic BP load was the proportion (%) of systolic BP readings ≥130 mm Hg during the daytime and ≥110 during the nighttime. Our primary endpoint was total mortality and major adverse cardiovascular endpoints (MACE). Statistics included Cox proportional models.

RESULTS

During a median follow-up of 8.3 years, 299 participants died and 210 experienced MACE. Each +2 mm Hg (corresponding to 1-standard deviation) higher 24-h systolic ARV (mean value, 9.0 ± 2.0 mm Hg) was associated with higher hazard ratios (HRs) for mortality by 1.28-fold (95% confidence interval [CI], 1.14–1.43) and for MACE by 1.24-fold (95% CI, 1.08–1.42). Each 30% higher 24-h systolic BP load (median value, 63%) was associated with mortality and MACE with HRs of 1.29 (95% CI, 1.15–1.46) and 1.28 (95% CI, 1.10–1.48); respectively. After models were additionally adjusted by BP level, only ARV was associated with mortality (HR, 1.17; 95% CI, 1.04–1.33) and MACE (HR, 1.16; 95% CI, 1.00–1.34).

CONCLUSIONS

High ARV and hypertensive loads in 24-h systolic BP were associated with mortality and cardiovascular risk, however, only ARV is associated independently of the BP level.
Efficacy of a mixed extract ofSalvia miltiorrhizaandPaeonia lactiflorain inhibiting the aging of vascular wall throughin vitroandin vivoexperiments
Authors: Son Juah , Cha Mi-Ran , Song Sukjin , Oh Byulnim , Bang Sangwoo , Cha Jinwook , Lim Sung Don , Yang Seo Young
Published: January 2024

Vascular wall aging has been strongly associated with cardiovascular diseases. Thus, this study aimed to investigate the efficacy of USCP-GVH-014, a mixed extract of Salvia miltiorrhiza Bunge and Paeonia lactiflora Pall., in inhibiting vascular wall aging through in vitro and in vivo experiments. The results revealed that USCP-GVH-014 inhibited abnormal cell proliferation, collagen overproduction, and MMP-2 and MMP-9 overexpression caused by various stimuli and recovered the antioxidant enzyme superoxide dismutase on human aortic smooth muscle cells. In addition, it inhibited the increase in ICAM-1 and VCAM-1 expression induced by tumor necrosis factor alpha on human aortic endothelial cells and prevented the aging of the vascular wall by regulating related proteins such as epidermal growth factor and interleukin-1ß. Furthermore, it reduced vascular aging in in vivo studies. These results demonstrate that USCP-GVH-014 effectively reduces vascular aging, thereby rendering it a potential therapeutic candidate for cardiovascular diseases.
GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function
Authors: Miller Danielle , Arias Ofir , Burstein David
Published: January 2024

GeNLP is a web application that enables exploring microbial gene “semantics” and predictions of uncharacterized gene families based on their genomic context. It utilizes a pre-trained language model to uncover gene relationships and allows users to access and utilize the data as well as make their own predictions through an interactive interface.

Availability and implementation

The web application is accessible from all browsers at: http://gnlp.bursteinlab.org/. All source codes are freely available from GitHub under the MIT license here: https://github.com/burstein-lab/genomic-nlp-server.
Scbean: a python library for single-cell multi-omics data analysis
Authors: Zhang Haohui , Wang Yuwei , Lian Bin , Wang Yiran , Li Xingyi , Wang Tao , Shang Xuequn , Yang Hui , Aziz Ahmad , Hu Jialu
Published: January 2024

Single-cell multi-omics technologies provide a unique platform for characterizing cell states and reconstructing developmental process by simultaneously quantifying and integrating molecular signatures across various modalities, including genome, transcriptome, epigenome, and other omics layers. However, there is still an urgent unmet need for novel computational tools in this nascent field, which are critical for both effective and efficient interrogation of functionality across different omics modalities. Scbean represents a user-friendly Python library, designed to seamlessly incorporate a diverse array of models for the examination of single-cell data, encompassing both paired and unpaired multi-omics data. The library offers uniform and straightforward interfaces for tasks, such as dimensionality reduction, batch effect elimination, cell label transfer from well-annotated scRNA-seq data to scATAC-seq data, and the identification of spatially variable genes. Moreover, Scbean’s models are engineered to harness the computational power of GPU acceleration through Tensorflow, rendering them capable of effortlessly handling datasets comprising millions of cells.

Availability and implementation

Scbean is released on the Python Package Index (PyPI) (https://pypi.org/project/scbean/) and GitHub (https://github.com/jhu99/scbean) under the MIT license. The documentation and example code can be found at https://scbean.readthedocs.io/en/latest/.
Delayed presentation of congenital sigmoid colon stenosis: a rare entity
Authors: Dahal Prajwal , Dawadi Kapil , Parajuli Sabina
Published: January 2024

Congenital sigmoid colon stenosis is a rare entity that can mimic Hirschsprung disease. Presentation of congenital colon stenosis is usually within first few weeks of life. Our case presented with features of distal bowel obstruction at 2 years of age with the history of chronic constipation and progressive abdominal distention from first week of life and bilious vomiting for the last 1 week. Clinical diagnosis of Hirschsprung disease was made. Contrast enhanced CT abdomen showed bowel obstruction with transition point at the level of proximal sigmoid colon. There was a short segment stenosis at the level of proximal sigmoid colon. Contrast enema showed stenosis at proximal sigmoid colon. The bowel distal to stenosis was normal in calibre. Similar findings were seen during surgery. Mesocolon was present in stenosed segment of the bowel. The resected stenotic segment showed adequate ganglion cells in histopathology.
Neuroinvasive Francisella tularensis Infection: Report of 2 Cases and Review of the Literature
Authors: Cash-Goldwasser Shama , Beeson Amy , Marzec Natalie , Ho Dora Y , Hogan Catherine A , Budvytiene Indre , Banaei Niaz , Born Donald E , Gephart Melanie H , Patel Jatinbhai , Dietrich Elizabeth A , Nelson Christina A
Published: January 2024

Background

Neuroinvasive infection with Francisella tularensis, the causative agent of tularemia, is rare. Establishing clinical suspicion is challenging if risk factors or clinical features classically associated with tularemia are absent. Tularemia is treatable with antibiotics; however, there are limited data to inform management of potentially fatal neuroinvasive infection.

Methods

We collected epidemiologic and clinical data on 2 recent US cases of neuroinvasive F. tularensis infection, and performed a literature review of cases of neuroinvasive F. tularensis infection published after 1950.

Results

One patient presented with focal neurologic deficits and brain lesions; broad-range molecular testing on resected brain tissue detected F. tularensis. The other patient presented with meningeal signs; tularemia was suspected based on animal exposure, and F. tularensis grew in cerebrospinal fluid (CSF) culture. Both patients received combination antibiotic therapy and recovered from infection. Among 16 published cases, tularemia was clinically suspected in 4 cases. CSF often displayed lymphocytic pleocytosis. Among cases with available data, CSF culture was positive in 13 of 16 cases, and F. tularensis antibodies were detected in 11 of 11 cases. Treatment typically included an aminoglycoside combined with either a tetracycline or a fluoroquinolone. Outcomes were generally favorable.

Conclusions

Clinicians should consider neuroinvasive F. tularensis infection in patients with meningitis and signs suggestive of tularemia or compatible exposures, lymphocyte-predominant CSF, unrevealing standard microbiologic workup, or lack of response to empiric bacterial meningitis treatment. Molecular testing, culture, and serologic testing can reveal the diagnosis. Favorable outcomes can be achieved with directed antibiotic treatment.
Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin
Authors: Venetz Jessica , Żygadłowska Olga M , Dotsios Nicky , Wallenius Anna J , van Helmond Niels A G M , Lenstra Wytze K , Klomp Robin , Slomp Caroline P , Jetten Mike S M , Veraart Annelies J
Published: January 2024

In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water–air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water–air fluxes remained below 0.6 mmol m−2 d−1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water–air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.
Height increment patterns in Pinus pinaster seedlings emerging in naturally regenerated gaps
Authors: de Frutos Sergio , Manso Rubén , Roig-Gómez Sonia , Ruiz-Peinado Ricardo , del Río Miren , Bravo-Fernández José Alfredo
Published: January 2024

The group selection cutting system provides a promising technique for transforming monospecific even-aged stands into uneven-aged, mixed stands. However, this system has scarcely been used to regenerate Mediterranean shade-intolerant species. In this study, we analyze the height increment patterns of Pinus pinaster seedlings emerging in naturally regenerated gaps. P. pinaster is a shade-intolerant pine species distributed throughout the Mediterranean basin. An experimental trial was established in a 50-year-old P. pinaster (maritime pine) plantation located in the mountains of central Spain. Gaps of two different sizes (diameter equal to 1.5 and 2.5 times the dominant height of the stand, 26 and 44 m, respectively) were opened during winter 2017–18. A total of 531 subplots with a 1-m radius were installed in spring 2018, distributed within the gaps as well as in control plots adjacent to the gaps. Seedlings were tagged individually and variables including height, along with other ecological variables, were collected twice a year (in spring and autumn), providing six time intervals for the development of our models. We applied seemingly unrelated regression to analyze the height growth in this polycyclic species, allowing us to model spring and autumn height increments at the same time. Our results showed that seedling height growth depended on the silvicultural treatment, meteorological conditions during the spring growth season, inter-specific scrub competition, position within the gap, and seedling characteristics, such as the ontogenetic development or the size of the seedling itself. This work, along with germination and survival analysis, aims to provide a holistic perspective on the suitability of the group selection cutting system to regenerate maritime pine stands, taking into account current and future climate change scenarios.
Epigenetic Regulation of Autophagy in Bone Metabolism
Authors: Zhang Yazhou , Wang Qianqian , Xue Hongjia , Guo Yujin , Wei Shanshan , Li Fengfeng , Gong Linqiang , Pan Weiliang , Jiang Pei
Published: January 2024

The skeletal system is crucial for supporting bodily functions, protecting vital organs, facilitating hematopoiesis, and storing essential minerals. Skeletal homeostasis, which includes aspects such as bone density, structural integrity, and regenerative processes, is essential for normal skeletal function. Autophagy, an intricate intracellular mechanism for degrading and recycling cellular components, plays a multifaceted role in bone metabolism. It involves sequestering cellular waste, damaged proteins, and organelles within autophagosomes, which are then degraded and recycled. Autophagy’s impact on bone health varies depending on factors such as regulation, cell type, environmental cues, and physiological context. Despite being traditionally considered a cytoplasmic process, autophagy is subject to transcriptional and epigenetic regulation within the nucleus. However, the precise influence of epigenetic regulation, including DNA methylation, histone modifications, and non-coding RNA expression, on cellular fate remains incompletely understood. The interplay between autophagy and epigenetic modifications adds complexity to bone cell regulation. This article provides an in-depth exploration of the intricate interplay between these two regulatory paradigms, with a focus on the epigenetic control of autophagy in bone metabolism. Such an understanding enhances our knowledge of bone metabolism-related disorders and offers insights for the development of targeted therapeutic strategies.
T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality
Authors: Zhang Shuwen , Yu Zheping , Sun Li , Liang Senmiao , Xu Fei , Li Sujuan , Zheng Xiliang , Yan Lijv , Huang Yinghong , Qi Xingjiang , Ren Haiying
Published: January 2024

Chinese bayberry (Myrica rubra or Morella rubra; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar ‘Zaojia’ using PacBio HiFi long reads. The resulting 292.60 Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151 bp region, harboring two MYB genes (MrChr6G07650 and MrChr6G07660), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.
A successful shift from thoracotomy to video-assisted thoracoscopic lobectomy for non-small cell lung cancer in a low-volume center
Authors: Asbjornsson Viktor , Johannsdottir Gyda , Myer Daniel , Runarsson Thorri Geir , Heitmann Leon Arnar , Oskarsdottir Gudrun N , Silverborn Per Martin , Hansen Henrik Jessen , Gudbjartsson Tomas
Published: January 2024

OBJECTIVES

Although video-assisted thoracoscopic surgery (VATS) lobectomy has become the gold standard for pulmonary resections of non-small-cell lung cancer (NSCLC), lobectomy is still performed via thoracotomy in many European and North American centres. VATS lobectomy was implemented overnight from thoracotomy in our low-volume centre in early 2019, after 1 senior surgeon undertook observership VATS-training overseas, and immediately became the mainstay of surgical treatment for NSCLC in Iceland. We aimed to investigate our short-term outcomes of VATS lobectomy.

METHODS

This was a retrospective study on all pulmonary resections for NSCLC in Iceland 2019–2022, especially focusing on VATS lobectomies, all at cTNM stage I or II. Data were retrieved from hospital charts, including information on perioperative complications, mortality, length of stay and operation time.

RESULTS

Out of 204 pulmonary resections, mostly performed by a single senior cardiothoracic surgeon, 169 were lobectomies (82.9%) with 147 out of 169 (87.0%) being VATS lobectomies. Anterolateral thoracotomy was used in 34 cases (16.7%), including 22 lobectomies (64.7%), and 5 (3.4%) conversions from VATS lobectomy. The median postoperative stay for VATS lobectomy was 4 days and the average operating time decreased from 155 to 124 min between the first and last year of the study (P < 0.001). The rate of major and minor complications was 2.7% and 15.6% respectively. One year survival was 95.6% and all patients survived 30 days postoperatively.

CONCLUSIONS

The implementation of VATS lobectomy has been successful in our small geographically isolated centre, serving a population of 390 000. Although technically challenging, VATS lobectomy was implemented fast for most NSCLC cases, with short-term outcomes that are comparable to larger high-volume centres.
Protozoan predation enhances stress resistance and antibiotic tolerance in Burkholderia cenocepacia by triggering the SOS response
Authors: Morón Álvaro , Tarhouchi Alaa E , Belinchón Iván , Valenzuela Juan M , de Francisco Patricia , Martín-González Ana , Amaro Francisco
Published: January 2024

Bacterivorous protists are thought to serve as training grounds for bacterial pathogens by subjecting them to the same hostile conditions that they will encounter in the human host. Bacteria that survive intracellular digestion exhibit enhanced virulence and stress resistance after successful passage through protozoa but the underlying mechanisms are unknown. Here we show that the opportunistic pathogen Burkholderia cenocepacia survives phagocytosis by ciliates found in domestic and hospital sink drains, and viable bacteria are expelled packaged in respirable membrane vesicles with enhanced resistance to oxidative stress, desiccation, and antibiotics, thereby contributing to pathogen dissemination in the environment. Reactive oxygen species generated within the protozoan phagosome promote the formation of persisters tolerant to ciprofloxacin by activating the bacterial SOS response. In addition, we show that genes encoding antioxidant enzymes are upregulated during passage through ciliates increasing bacterial resistance to oxidative radicals. We prove that suppression of the SOS response impairs bacterial intracellular survival and persister formation within protists. This study highlights the significance of protozoan food vacuoles as niches that foster bacterial adaptation in natural and built environments and suggests that persister switch within phagosomes may be a widespread phenomenon in bacteria surviving intracellular digestion.
A national survey of digital health company experiences with electronic health record application programming interfaces
Authors: Barker Wesley , Maisel Natalya , Strawley Catherine E , Israelit Grace K , Adler-Milstein Julia , Rosner Benjamin
Published: January 2024

Objectives

This study sought to capture current digital health company experiences integrating with electronic health records (EHRs), given new federally regulated standards-based application programming interface (API) policies.

Materials and methods

We developed and fielded a survey among companies that develop solutions enabling human interaction with an EHR API. The survey was developed by the University of California San Francisco in collaboration with the Office of the National Coordinator for Health Information Technology, the California Health Care Foundation, and ScaleHealth. The instrument contained questions pertaining to experiences with API integrations, barriers faced during API integrations, and API-relevant policy efforts.

Results

About 73% of companies reported current or previous use of a standards-based EHR API in production. About 57% of respondents indicated using both standards-based and proprietary APIs to integrate with an EHR, and 24% worked about equally with both APIs. Most companies reported use of the Fast Healthcare Interoperability Resources standard. Companies reported that standards-based APIs required on average less burden than proprietary APIs to establish and maintain. However, companies face barriers to adopting standards-based APIs, including high fees, lack of realistic clinical testing data, and lack of data elements of interest or value.

Discussion

The industry is moving toward the use of standardized APIs to streamline data exchange, with a majority of digital health companies using standards-based APIs to integrate with EHRs. However, barriers persist.

Conclusion

A large portion of digital health companies use standards-based APIs to interoperate with EHRs. Continuing to improve the resources for digital health companies to find, test, connect, and use these APIs “without special effort” will be crucial to ensure future technology robustness and durability.
Loss of 24-hydroxylated catabolism increases calcitriol and fibroblast growth factor 23 and alters calcium and phosphate metabolism in fetal mice
Authors: Bennin David , Hartery Sarah A , Kirby Beth J , Maekawa Alexandre S , St-Arnaud René , Kovacs Christopher S
Published: January 2024

Calcitriol circulates at low levels in normal human and rodent fetuses, in part due to increased 24-hydroxylation of calcitriol and 25-hydroxyvitamin D by 24-hydroxylase (CYP24A1). Inactivating mutations of CYP24A1 cause high postnatal levels of calcitriol and the human condition of infantile hypercalcemia type 1, but whether the fetus is disturbed by the loss of CYP24A1 is unknown. We hypothesized that loss of Cyp24a1 in fetal mice will cause high calcitriol, hypercalcemia, and increased placental calcium transport. The Cyp24a1+/− mice were mated to create pregnancies with wildtype, Cyp24a1+/−, and Cyp24a1 null fetuses. The null fetuses were hypercalcemic, modestly hypophosphatemic (compared to Cyp24a1+/− fetuses only), with 3.5-fold increased calcitriol, 4-fold increased fibroblast growth factor 23 (FGF23), and unchanged parathyroid hormone. The quantitative RT-PCR confirmed the absence of Cyp24a1 and 2-fold increases in S100g, sodium–calcium exchanger type 1, and calcium-sensing receptor in null placentas but not in fetal kidneys; these changes predicted an increase in placental calcium transport. However, placental 45Ca and 32P transport were unchanged in null fetuses. Fetal ash weight and mineral content, placental weight, crown-rump length, and skeletal morphology did not differ among the genotypes. Serum procollagen 1 intact N-terminal propeptide and bone expression of sclerostin and Blgap were reduced while calcitonin receptor was increased in nulls. In conclusion, loss of Cyp24a1 in fetal mice causes hypercalcemia, modest hypophosphatemia, and increased FGF23, but no alteration in skeletal development. Reduced incorporation of calcium into bone may contribute to the hypercalcemia without causing a detectable decrease in the skeletal mineral content. The results predict that human fetuses bearing homozygous or compound heterozygous inactivating mutations of CYP24A1 will also be hypercalcemic in utero but with normal skeletal development.
Mapping of geological structures and sediment thickness from analysis of aeromagnetic data over the Obudu Basement Complex of Nigeria
Authors: Ekwok Stephen E , Eldosuoky Ahmed M , Thompson Edward A , Ojong Romeo A , George Anthony M , Alarifi Saad S , Kharbish Sherif , Andráš Peter , Akpan Anthony E
Published: January 2024

In this study, geologic structures, as well as attendant orientations and sediment thickness, in the Nigerian Obudu Complex were delineated using the Centre for Exploration Targeting (CET), and depth determination methods such as source parameter imaging (SPI) and standard Euler deconvolution (SED). The CET, SPI, and SED procedures were applied on the total magnetic intensity data. Also, the enhanced TMI data using analytic signal, first-vertical derivative, total-horizontal derivative, and tilt-angle derivative filters were further subjected to CET operation, with the aim of mapping both subtle and prominent lineaments. In general, mapped geologic structures trends in the NE–SW, NNE–SSW, E–W, and N–S directions. Overall, the dominant geologic structural orientations of NE–SW and NNE–SSW reflect the regional strike orientation. The regional striking of the lineation, which is caused by the Pan-African orogeny and subsequent post-orogenic processes, has an impact on these orientations. The N–S and E–W structural deviations from the main NE–SW and NNE–SSW trends are initiated by the YGS of the post-orogenic events. Overall, these complex geologic structures are probable sites for metallogenic minerals.
Review of Panel Discussion on Digital, Media and Information Literacy—Report of the Office of the United Nations High Commissioner for Human Rights
Authors: Lee Josephina
Published: January 2024

This review considers the Panel Discussion on Digital, Media and Information Literacy—Report of the Office of the UN High Commissioner for Human Rights, and explores the report’s key implications for human rights practitioners and their organizations.
Beijing Internet Court recognizes copyright in AI-generated image
Authors: Wen Tingting
Published: January 2024

In the initial instance involving artificial intelligence (AI)-generated images in China, the Beijing Internet Court determined that AI-generated images are considered protectable works, and the AI user is recognized as the author.
Simulating the population impact of interventions to reduce racial gaps in breast cancer treatment
Authors: Yanguela Juan , Jackson Bradford E , Reeder-Hayes Katherine E , Roberson Mya L , Rocque Gabrielle B , Kuo Tzy-Mey , LeBlanc Matthew R , Baggett Christopher D , Green Laura , Laurie-Zehr Erin , Wheeler Stephanie B
Published: January 2024

Background

Inequities in guideline-concordant treatment receipt contribute to worse survival in Black patients with breast cancer. Inequity-reduction interventions (eg, navigation, bias training, tracking dashboards) can close such treatment gaps. We simulated the population-level impact of statewide implementation of inequity-reduction interventions on racial breast cancer inequities in North Carolina.

Methods

Using registry-linked multipayer claims data, we calculated inequities between Black and White patients receiving endocrine therapy (n = 12 033) and chemotherapy (n = 1819). We then built cohort-stratified (endocrine therapy and chemotherapy) and race-stratified Markov models to simulate the potential increase in the proportion of patients receiving endocrine therapy or chemotherapy and subsequent improvements in breast cancer outcomes if inequity-reducing intervention were implemented statewide. We report uncertainty bounds representing 95% of simulation results.

Results

In total, 75.6% and 72.1% of Black patients received endocrine therapy and chemotherapy, respectively, over the 2006-2015 and 2004-2015 periods (vs 79.3% and 78.9% of White patients, respectively). Inequity-reduction interventions could increase endocrine therapy and chemotherapy receipt among Black patients to 89.9% (85.3%, 94.6%) and 85.7% (80.7%, 90.9%). Such interventions could also decrease 5-year and 10-year breast cancer mortality gaps from 3.4 to 3.2 (3.0, 3.3) and from 6.7 to 6.1 (5.9, 6.4) percentage points in the endocrine therapy cohorts and from 8.6 to 8.1 (7.7, 8.4) and from 8.2 to 7.8 (7.3, 8.1) percentage points in the chemotherapy cohorts.

Conclusions

Inequity-focused interventions could improve cancer outcomes for Black patients, but they would not fully close the racial breast cancer mortality gap. Addressing other inequities along the cancer continuum (eg, screening, pre- and postdiagnosis risk factors) is required to achieve full equity in breast cancer outcomes.
A new method of solving plane-strain boundary value problems for the double slip and rotation model
Authors: Alexandrov Sergei , Lyamina Elena , Jeng Yeau-Rean
Published: January 2024

A method of solving plane-strain boundary value problems for a reduced version of the double slip and rotation model is developed. It is assumed that the intrinsic spin vanishes. Elastic strains are neglected. The Mohr–Coulomb yield criterion is adopted. An analogy between the solutions for this model and classical rigid plastic solutions of pressure-independent plasticity is revealed. The method is based on introducing auxiliary variables that satisfy the equation of telegraphy in regions where both families of characteristics are curved. Therefore, Riemann's method can conveniently be applied to solving boundary value problems. The method is employed for analyzing the processes of plane-strain drawing and extrusion through a wedge-shaped die. Friction is neglected. The solution is given in terms of ordinary integrals. The effect of the angle of internal friction on processes’ parameters is revealed. The solution reduces to available solutions of pressure-independent plasticity if the angle of internal friction vanishes.