bluuebunny/crossref_metadata_2025 huggingface dataset:
ENUBET: a monitored neutrino beam for the precision era of neutrino physics
Authors: Iacob F , Acerbi F , Angelis I , Bonesini M , Branca A , Brizzolari C , Brunetti G , Calviani M , Capelli S , Carturan S , Catanesi M G , Cecchini S , Charitonidis N , Cindolo F , Collazuol G , Corso F Dal , Delogu C , Rosa G De , Falcone A , Goddard B , Gola A , Jollet C , Kain V , Klicek B , Kudenko Y , Lampoudis Ch , Laveder M , Longhin A , Ludovici L , Lutsenko E , Magaletti L , Mandrioli G , Margotti A , Mascagna V , Mauri N , Meazza L , Meregaglia A , Mezzetto M , Nessi M , Paoloni A , Pari M , Parozzi E G , Pasqualini L , Paternoster G , Patrizii L , Pozzato M , Prest M , Pupilli F , Radicioni E , Riccio C , Ruggeri A C , Sampsonidis D , Scian C , Sirri G , Stipcevic M , Tenti M , Terranova F , Torti M , Tzamarias S E , Vallazza E , Velotti F , Votano L
Published: February 2022

The ENUBET ERC project, also included in the CERN Neutrino Platform as NP06/ENUBET, is developing a new neutrino beam based on conventional techniques in which the flux and the flavor composition are known with unprecedented precision (O (1%)). Such a goal is accomplished monitoring the associated charged leptons produced in the decay region of the ENUBET facility. Positrons and muons from kaon decays are measured by a segmented calorimeter instrumenting the walls of the decay tunnel, while muon stations after the hadron dump can be used to monitor the neutrino component from pion decays. Furthermore, the narrow momentum width (<10%) of the beam provides a precise measurement (O (10%)) of the neutrino energy on an event by event basis, thanks to its correlation with the radial position of the interaction at the neutrino detector. ENUBET is therefore an ideal facility for a high precision neutrino cross-section measurement at the GeV scale, that could enhance the discovery potential of the next-generation of long baseline experiments. It is also a powerful tool for testing the sterile neutrino hypothesis and to investigate possible non-standard interactions.
The optical simulation model of the DarkSide-20k Veto detector
Authors: Türkoülu Cenk , Choudhary Sarthak
Published: February 2022

DarkSide-20k is a rare-event search experiment aimed at finding signals of dark matter particles. It is a dual-phase detector that registers ionisation and scintillation signals originating from the particles interacting with the liquid argon detector medium. It is enclosed in a single-phase liquid argon neutron veto tank, equipped with Gd-loaded panels for capturing neutrons. Since vetoing and particle identification are carried out using the light signal, it is crucial to maximise the light yield. Light collection efficiency depends on optical properties of the detector and particularly for the veto detector, which has a photosensor coverage of the order of a per cent, the reflectivity of the walls has a big impact. To quantify the amount of collected light, a comprehensive Geant4 simulation is performed, which uses optical characterisation data. In this work, a detailed description of the optics model for the veto of the experiment will be discussed.
Neutrino quantum decoherence engendered by neutrino decay to photons, familons and gravitons
Authors: Lichkunov Alexey , Stankevich Konstantin , Studenikin Alexander , Vyalkov Maxim
Published: February 2022

We developed the previously proposed theoretical framework based on the quantum field theory of open systems applied to neutrinos. Within this framework we have considered the neutrino evolution and neutrino flavour oscillations taking into account for the decay of a heavier neutrino state to a lighter neutrino state and to a massless particle, namely photons, dark photons, axion-like particles and gravitons. We have shown that the neutrino evolution accounting for the decays will be governed by the Lindblad master equation, in which the decoherence parameters are proportional to the neutrino decay rate.
Characterization of the DUNE photodetectors and study of the event burst phenomenon
Authors: Minotti Alessandro
Published: February 2022

The Deep Underground Neutrino Experiment (DUNE) is an upcoming neutrino physics experiment that will answer some of the most compelling questions in particle physics and cosmology. The DUNE far detectors employ silicon photomultipliers (SiPMs) to detect light produced by charged particles interacting in a large liquid argon time projection chamber (LArTPC). The SiPMs are photosensors consisting of an array of single-photon avalanche diodes (SPAD) operating in Geiger mode. Their high sensitivity and dynamic range, as well as the possibility to fill large surfaces with high-granularity sensors, makes them an ideal choice for DUNE. An international consortium of research groups is currently engaged in a systematic comparison of the performances of the SiPM models that have been custom developed for DUNE by two manufacturers. Such detailed studies, which include gain measurements and a structure study of the dark count rate at 77 K, are meant to determine the best choice of the photodetection system for DUNE, as well as characterize the response of the chosen detectors for the DUNE simulation. Moreover, an investigation of a newly observed phenomenon, in which quick bursts of tens of events at close range are collected in individual SiPMs, is being carried out, which potentially impacts the design of future models and their implementation in particle physics experiments.
Predicting flood damage probability across the conterminous United States
Authors: Collins Elyssa L , Sanchez Georgina M , Terando Adam , Stillwell Charles C , Mitasova Helena , Sebastian Antonia , Meentemeyer Ross K
Published: February 2022

Floods are the leading cause of natural disaster damages in the United States, with billions of dollars incurred every year in the form of government payouts, property damages, and agricultural losses. The Federal Emergency Management Agency oversees the delineation of floodplains to mitigate damages, but disparities exist between locations designated as high risk and where flood damages occur due to land use and climate changes and incomplete floodplain mapping. We harnessed publicly available geospatial datasets and random forest algorithms to analyze the spatial distribution and underlying drivers of flood damage probability (FDP) caused by excessive rainfall and overflowing water bodies across the conterminous United States. From this, we produced the first spatially complete map of FDP for the nation, along with spatially explicit standard errors for four selected cities. We trained models using the locations of historical reported flood damage events (n = 71 434) and a suite of geospatial predictors (e.g. flood severity, climate, socio-economic exposure, topographic variables, soil properties, and hydrologic characteristics). We developed independent models for each hydrologic unit code level 2 watershed and generated a FDP for each 100 m pixel. Our model classified damage or no damage with an average area under the curve accuracy of 0.75; however, model performance varied by environmental conditions, with certain land cover classes (e.g. forest) resulting in higher error rates than others (e.g. wetlands). Our results identified FDP hotspots across multiple spatial and regional scales, with high probabilities common in both inland and coastal regions. The highest flood damage probabilities tended to be in areas of low elevation, in close proximity to streams, with extreme precipitation, and with high urban road density. Given rapid environmental changes, our study demonstrates an efficient approach for updating FDP estimates across the nation.
Categorization of plastic debris on sixty-six beaches of the Laurentian Great Lakes, North America
Authors: Arturo Ian A , Corcoran Patricia L
Published: February 2022

The Laurentian Great Lakes system is a major global sink for plastic debris. An area of 10 m2 on each of sixty-six Great Lakes beaches was sampled for large micro-, meso- and macroplastic items. A total of 21 592 plastic items were collected and categorized. Pre-production plastic pellets were the most abundant debris type, accounting for 58.3% of the total count. The remaining 42.7% of the debris items are the focus of this study. Detailed, multi-step characterization was performed with the plastics being categorized using physical identification, known usage, and Fourier transform infrared spectroscopy (FTIR). Values of 805.5 items m−2 at Baxter Beach in Sarnia, Ontario, Canada, and 688.1 items m−2 at Bronte Beach in Oakville, Ontario, Canada are the highest of all sampling locations. Sampling sites on only three beaches contained no plastic debris: Bay City in Michigan, U.S.A., Presque Isle State Park in Erie, Pennsylvania, U.S.A. and Pebble Beach in Marathon, Ontario, Canada. The plastic items sampled were mainly large microplastics (68.4% of total) with a total of 1477.5 items m−2, followed by mesoplastics (27.3% of total) with 598.8 items m−2, and macroplastics (4.3% of total) with 91.9 items m−2. By mass, the microplastic fraction accounted for 25.61 g m2 (14.1%), the mesoplastic for 47.06 g m2 (25.9%), and macroplastic for 109.3 g m2 (60.1%). A total of 3004 items were determined as specific polymers based on physical properties, known polymer usage, Resin Identification Code, and FTIR. A total of 1227 plastic items (40.8% of total) were identified as expanded polystyrene. The 49 most common items, excluding pellets, were scored using a matrix scoring technique to determine their potential general origin. It was determined that these items mostly originated from shoreline and urban sources, whereas pellets originated from the plastics industry.
Cellulolytic fungi modify the nitrogen, phosphorus, and potassium contents of organic fertilizers
Authors: Fikrinda F , Marlina M , Khalil M
Published: February 2022

Cellulolytic fungi are involved in releasing nutrients from organic sources. The objective of this study was to determine the effect of cellulolytic fungi on the total nitrogen (N), total phosphorus (P), and total potassium (K) contents in different organic fertilizers. This study was arranged in randomized block design 3 X 3 with three replications. There were two factors, cellulolytic fungi (Talaromyces pinophilus strain MR107, Penicillium sp. isolate SR18, and Purpureocillium lilacinum isolate PIGD23i) and organic fertilizers (cow manure, compost, and vermicompost). The results indicated that Penicillium sp. isolate SR18 had a better effect than other cellulolytic fungi species on tot. N, tot. P and tot. K contents of cow manure; tot. N and tot. K contents of compost; and tot. P content of vermicompost while P. lilacinum isolate PIGD23i showed a better effect on tot. N and tot. K contents of vermicompost. The highest tot. N, and tot. K contents were found in P. lilacinum isolate PIGD23i-inoculated vermicompost while the tot. P content was in Penicillium sp. isolate SR18-inoculated vermicompost. Overall, adding cellulolytic fungi is an alternative way to improve the nutrient content of organic fertilizer.
Changes in functional properties during fermentation of Amorphophallus paeoniifolius (Dennst.) Nicolson yam using Lactobacillus plantarum
Authors: Syah I T , Irundu D , Bahmid N A , Indrastuti  , Karim I
Published: February 2022

The purpose of this study was to see how inoculum loading (2 and 5% v/v) and fermentation period (0–72 h) affected the functional properties ofA. paeoniifolius(Dennst.) Nicolson yam flour.L. plantarumfermentation was used to ferment the sliced yam. In general, swelling power of modified flour increased along with the increasing of inoculum and fermentation time but not significant, while the water solubility index reduced significantly by fermentation. The water absorption capacity of flour increased significantly as inoculum concentration and fermentation period were increased, and then decreased with the length of the fermentation process. Bulk density implied that the fermentation process formed an open structure of starch granule with a higher proportion of void spaces. The FTIR analysis showed the modification of functional groups of starch that indicates the change of physicochemical properties along the fermentation process due to the interaction ofL. plantarum. The color of the treated flour whiter than control makes its application for various food products will be wider. This result suggested that fermentation by 5%L. plantarumwithin 48 h could provide a greater extent of flour such as processed cheese, sausage, dough, and baked products.
Grain yield and yield component trait association and salinity tolerance of rice lines under mild saline stress condition
Authors: Nafisah  , Sitaresmi T. , Gunarsih C. , Hairmansis A.
Published: February 2022

The research was aimed to study yield and yield component trait association and salinity tolerance of rice genotypes under mild saline stress condition. The activity was done in Soge, Kandanghaur Indramayu district, West Java Indonesia, from July to November 2020. The material consisted of 150 genotypes including sixteen check varieties represented high yield popular rice varieties and salinity tolerance rice varieties. The alpha lattice design with two replications with a 4 m2 plot size was used in this experiment. A total of three seedlings that was twenty-one days old was manually transplanted in one hole with a 25 x 25 cm planting space. The result showed that under mild saline stress condition, there was no association between grain yield and salinity tolerance at the seedling stage. The grain yield positively correlated with a tolerance of genotype at the vegetative stage, plant height, tiller number, spikelet fertility and negatively associated with unfilled grain number. These traits can be used as indirect selection criteria for high grain yield under mild saline stress condition.
Prospect of sorghum development as corn substitution in Indonesia
Authors: Pujiharti Y , Paturohman E , Ikhwani
Published: February 2022

This paper explores the opportunities for the development of sorghum to reduce imports of corn. Besides being the primary raw material for poultry feed, corn is the second staple-food ingredient after rice. Still, the increase in corn production is not in line with the demand for corn due to the increasing population. This condition has resulted in the need for corn to be imported, while the government has imposed an import ban since 2017. It is necessary to have other commodities that can substitute corn as food as sorghum. Sorghum farming produces not only sorghum seeds but also plant waste which can use for a ruminant feed so that the availability of ruminant feed continues. Sorghum farming needs to be developed so that the availability of food and feed can sustain. The development of sorghum should be in areas where there is a feed industry to ensure the sorghum market for farmers and the availability of raw materials. The development can also be in areas that have long consumed sorghum (local food).
Competitiveness analysis of Indonesian processes and non-processed agricultural commodities in the ASEAN Region
Authors: Tety E , Kurnia D , Andriani Y
Published: February 2022

The commitment of the ASEAN Economic Community opens opportunities up for member countries including Indonesia to improve the trade balance, especially in processed and non-processed agricultural products. These opportunities should be followed by increasing the competitiveness of each country. The purpose of this study was to analyze the development of exports of processed and non-processed Indonesian agricultural products in the ASEAN region and the competitiveness of exports of agricultural products in ASEAN countries to the main destination countries. TSI analysis was used to determine the development of exports, while the Constant Market Share (CMS) and Revealed Comparative Advantage (RCA) approaches are used to analyze the competitiveness and competitive advantages of each ASEAN member country. The results showed that Indonesia was in the top position for the export of agricultural processed products in 2009 with a TSI reaching 0.87. Whereas non-processed agricultural products led by Thailand with TSI reached 0.89. Increased competitiveness of processed and non-processed products is more influenced by increased demand in export destination countries. The RCA index of non - processed agricultural products in Thailand reached a peak in 2014 at a 3.2 position, while Indonesia had the highest RCA index in agricultural processed products which reached 8.80. This shows that Indonesia has comparative advantages in agricultural processed products compared to other countries in ASEAN.
Utilization of tofu waste from Indonesian small scale industry as fish feed through a fermentation process
Authors: Mulyasari  , Subaryono  , Yosmaniar
Published: February 2022

Tofu waste is a by-product from the soybean processing industry like tofu and tempeh in Indonesia. The high amount of waste from tofu processing creates problems for the environment, both in aesthetics and odor. Therefore, the utilization and treatment of waste from tofu processing industry activities is needed to reduce the negative impact of the resulting waste. One of them is to use it as a raw material for fish feed. Tofu waste has a good nutrient content (protein content is around 21.3 - 27%), so a potential source of fish raw material. However, tofu waste has low digestibility because of its high fiber (16-23%) and antinutrient substances content. Therefore, improving the quality of tofu waste by fermentation was needed. Fermentation can change a substrate or raw material into the desired product with better quality. It can reduce the levels of crude fiber, increase digestibility, and increase levels of soluble protein and crude protein from raw material. This research aimed to evaluate the quality of tofu waste fermented using Bacillus sp PAS7 as raw material for fish feed production. This research used a completely randomized design (CRD) with four treatments and three replicates. The treatment for determining inoculum doses used concentrations of 0, 2, 4, and 6% per gram (weight) of tofu waste (v / w). The time of the fermentation process was three days at 37oC. The parameters measured were reducing sugar, dissolved protein, proximate analysis, and in vitro protein digestibility. The results showed that tofu waste fermentation using Bacillus sp PAS7 isolate improved the nutrient quality of the material. It can be seen from the increased levels of dissolved glucose and protein, decreased fiber content, and increased in vitro protein digestibility. Fermentation using Bacillus sp PAS7 with a dose of 2% was adequate to improve the quality of tofu waste.
Potential use of Lactiplantibacillus plantarum strains for fermentation of fat milk
Authors: Nikitina E
Published: February 2022

The ability of potentially probiotic strains Lactiplantibacillus plantarum AG9 and AG10 to influence the quality of fat cow’s milk was studied. It was found that L. plantarum strains AG9 and AG10 showed high coagulation ability, actively ferment lactose and accumulate lactic acid. The strain Lactiplantibacillus plantarum AG10 is able to reduce the level of fat during fermentation, which is a show of lipotolytic effect. The texture characteristics of fermented milk produced with the use of these strains are excellent. L. plantarum strains both during and after fermentation survived well in fermented milk, indicating that the milk medium is a suitable substrate for this species. The results obtained at this stage of the study indicate the promising use as a co-culture in the technology of sour milk products.
Mapping of sustainable warehouse process in the agro-hub Banten using business process modelling notation
Authors: Wahyuni F D , Najah Z , Santoso M I
Published: February 2022

Study of sustainable warehousing management through modelling process bussiness in Agro-hub was needed as issue of environmentally-friendly way of warehouse management appeared. Agro-hub was distribution centre integrated with logistics, warehouses, packaging houses and digital markets. Warehouse processes include receiving, data records, packing, and inventory and logistics. This researched was aimed to designed sustainable warehouse process in the Agro-hub Banten. The modelling method was using Business Process Modelling Notation. The collecting data was done by observation, in-depth interview and documentation review. Results of this study are mapping of material acceptance process (purchasing), dara record process, and inventry and packing practices.
Predicting personalised and progressive adaptive dose escalation to gross tumour volume using knowledge-based planning models for inoperable advanced-stage non-small cell lung cancer patients treated with volumetric modulated arc therapy
Authors: Tambe Nilesh S , Pires Isabel M , Moore Craig , Wieczorek Andrew , Upadhyay Sunil , Beavis Andrew W
Published: February 2022

Objectives. Increased radiation doses could improve local control and overall survival of lung cancer patients, however, this could be challenging without exceeding organs at risk (OAR) dose constraints, especially for patients with advanced-stage disease. Increasing OAR doses could reduce the therapeutic ratio and quality of life. It is therefore important to investigate methods to increase the dose to target volume without exceeding OAR dose constraints. Methods. Gross tumour volume (GTV) was contoured on synthetic computerised tomography (sCT) datasets produced using the Velocity adaptive radiotherapy software for eleven patients. The fractions where GTV volume decreased compared to that prior to radiotherapy (reference plan) were considered for personalised progressive dose escalation. The dose to the adapted GTV (GTVAdaptive) was increased until OAR doses were affected (as compared to the original clinical plan). Planning target volume (PTV) coverage was maintained for all plans. Doses were also escalated to the reference plan (GTVClinical) using the same method. Adapted, dose-escalated, plans were combined to estimate accumulated dose, D99 (dose to 99%) of GTVAdapted, PTV D99 and OAR doses and compared with those in the original clinical plans. Knowledge-based planning (KBP) model was developed to predict D99 of the adapted GTV with OAR doses and PTV coverage kept similar to the original clinical plans; prediction accuracy and model verification were performed using further data sets. Results. Compared to the original clinical plan, the dose to GTV was significantly increased without exceeding OAR doses. Adaptive dose-escalation increased the average D99 to GTVAdaptive by 15.1Gy and 8.7Gy compared to the clinical plans. The KBP models were verified and demonstrated prediction accuracy of 0.4% and 0.7% respectively. Conclusion. Progressive adaptive dose escalation can significantly increase the dose to GTV without increasing OAR doses or compromising the dose to microscopic disease. This may increase overall survival without increasing toxicities.
The role of trust in public acceptability of energy projects: Integrity versus competence
Authors: Liu Lu , Vrieling Leonie , Perlaviciute Goda , Bouman Thijs , Steg Linda
Published: February 2022

Public acceptability of energy projects depends on people’s trust in agents responsible for those projects. We examined to what extent different dimensions of trust, notably integrity- and competence-based trust, are associated with public acceptability of real ongoing energy projects associated with acute risks and other consequences. A series of questionnaire studies in the Netherlands revealed that both integrity- and competence-based trust were positively associated with public acceptability of natural gas extraction which causes earthquakes in the region. Yet, integrity-based trust was more strongly and consistently associated with public acceptability of the natural gas extraction compared to competence-based trust. The findings were rather consistent across four different measurement phases. We discuss the theoretical and practical implications of our findings.
Recent developments in RAM based MWCNT composite materials: a short review
Authors: Yeswanth I V S , Jha Kanishka , Bhowmik Shantanu , Kumar Rajeev , Sharma Shubham , Ilyas R A
Published: February 2022

The need to develop radar absorbing materials (RAMs) that meet the structural requirement of defense applications is growing swiftly, due to the extensive use of electromagnetic waves in Radar. With the major developments and extensive use of Radar in military applications, the role of Radar absorbing, light weight and high strength structures has become a prime objective for researcher working on the development of RAMs. Various composites have been developed by using reinforcements which are dielectric, such as carbon nanotubes (CNT), magnetic materials like ferrites, that have been extensively used for reinforcement when developing RAMs. Ferromagnetic materials have a high density and can only achieve a narrow bandwidth of absorption. CNT have very good electrical, mechanical and thermal properties and can achieve high dielectric losses but their complex synthesis process is a barrier to commercial applications. Research on reinforcing multi-walled carbon nanotubes (MWCNT) with ferrites and metal oxides can also be extended to the study of thermoplastic polymers like polyether ether ketone and polyaryletherketone, which are gaining prominence in aeronautical applications, owing to their superior mechanical and low moisture absorbing properties. Further research can be carried out on reinforcing metal oxides, as metal oxides, when reinforced with MWCNT enhance the dielectric properties which improve the reflection losses as reported in a few studies.
Historians and Their Publics, Then and Now
Authors: Jones Jacqueline
Published: February 2022

The American Historical Association annual presidential addresses provide evidence of transformations in the profession and the discipline from the founding of the association in 1884. It was not until the late 1970s that AHA presidents began to explore the histories of women and people of color in any depth; before then, addresses gave short shrift to whole swaths of the human population, and many of these talks promoted a triumphalist view of United States history. Today people outside the academy encounter cutting-edge historical scholarship by way of their daily newspaper, blogs and online news sites, TV and films, the Broadway stage, historic places, debates over renaming streets and removing statues, and genealogy projects. At the same time, historians face challenges from budget-cutting administrators (in universities, libraries, and museums) and from cynical politicians who seek to replace truth with myth, in the process roiling state legislators and members of local school boards. Consequently, historians today contend with two major opposing forces—on the one hand, a proliferation of lively venues that bring inclusive stories about the past to a wider audience, and, on the other, political conditions that lead to the intimidation of historians regardless of where they work. In the face of these challenges, the AHA must continue its robust advocacy work on behalf of all historians.
Fused Lateral Clitoral Hood and Labia Minora: New Classification Based on Anatomic Variation of the Clitoral Hood–Labia Minora Complex and Simple Surgical Management
Authors: Xia Zenan , Liu Chang-Yi , Zhang Mingzi , Zhang Yuwei , Guan Ai , Li Yunzhu , Yu Nanze , Liu Zhifei , Zeng Ang , Si Loubin , Long Fei , Long Xiao , Zhu Lin
Published: February 2022

Background

Existing classifications of the clitoral hood–labia minora complex (CLC) have neglected its integrity and anatomic variation, resulting in failure to optimize approaches tailored to individuals.

Objectives

The aim of this study was to present a new classification system for comprehensive evaluation of variations of the CLC and to introduce a simple surgical approach for the fused type.

Methods

Anatomic variations of the CLC were classified into 3 types: isolated labia minora or lateral clitoral hood hypertrophy (Type 1); conventional combined hypertrophy (Type 2); and fused lateral clitoral hood and labia minora (Type 3). A modified procedure for the fused type was performed in 4 steps: the anterior border of labia minora was defined first, then the hypertrophic lateral clitoral hood and labia minora were each removed separately, and finally the junction region was trimmed. Satisfaction questionnaires were administered during follow-ups.

Results

Among all 301 patients (602 sides), Type 2 was the most common variation (285 sides, 47.3%). Type 3 variations in 67 patients (105 sides, 17.5%) were identified, and 77.6% of these patients answered the questionnaires 3 months after surgery. For patients with type 3 variations, the satisfaction rate in the 4-step excision group was 91.7%, which was significantly higher than that in the wedge excision group (56.3%) (P = 0.01). The complication rate of the 4-step excision was 2.5%.

Conclusions

Preoperative evaluation based on the new classification facilitated recognition of variations of the CLC, especially of the fused type. The 4-step excision is a simple, effective, and safe approach to treat the fused variation with high satisfaction.

Level of Evidence: 4
FitDock: protein–ligand docking by template fitting
Authors: Yang Xiaocong , Liu Yang , Gan Jianhong , Xiao Zhi-Xiong , Cao Yang
Published: February 2022

Protein–ligand docking is an essential method in computer-aided drug design and structural bioinformatics. It can be used to identify active compounds and reveal molecular mechanisms of biological processes. A successful docking usually requires thorough conformation sampling and scoring, which are computationally expensive and difficult. Recent studies demonstrated that it can be beneficial to docking with the guidance of existing similar co-crystal structures. In this work, we developed a protein–ligand docking method, named FitDock, which fits initial conformation to the given template using a hierarchical multi-feature alignment approach, subsequently explores the possible conformations and finally outputs refined docking poses. In our comprehensive benchmark tests, FitDock showed 40%–60% improvement in terms of docking success rate and an order of magnitude faster over popular docking methods, if template structures exist (> 0.5 ligand similarity). FitDock has been implemented in a user-friendly program, which could serve as a convenient tool for drug design and molecular mechanism exploration. It is now freely available for academic users at http://cao.labshare.cn/fitdock/.
Precise paternal ancestry of hybrid unisexual ZW lizards (genus Darevskia: Lacertidae: Squamata) revealed by Z-linked genomic markers
Authors: Yanchukov Alexey , Tarkhnishvili David , Erdolu Meriç , Şahin Mehmet Kürşat , Candan Kamil , Murtskhvaladze Marine , Gabelaia Mariam , Iankoshvili Giorgi , Barateli Natia , Ilgaz Çetin , Kumlutaş Yusuf , Matur Ferhat , Çolak Faruk , Arakelyan Marine , Galoyan Eduard
Published: February 2022

We genotyped multiple populations of all seven parthenogenetic species of rock lizards, genus Darevskia, as well as their putative sexual parental populations, using double digest RAD-sequencing genomic markers. Taking advantage of the conserved homology of the ZW/ZZ sex chromosomes among lacertid lizards, we aligned our short sequence reads to a reference Z chromosome assembly of the common wall lizard Podarcis muralis. This provided unique insight into the origin of all-female hybrid populations, which inherited their single Z chromosome exclusively from a paternal ancestor. The mapped Z-linked loci were used to construct a robust time-calibrated phylogeny. In each parent–offspring species pair, the geographically nearest population of the paternal species was identified as the most likely ancestor of the respective parthenogen, mirroring the trend observed previously on the maternal side in mitochondrial DNA. The estimated splits between the sampled paternal sexual ancestors and their daughter species occurred much earlier than suggested previously and during two narrow time periods: (1) the parthenogenetic Darevskia armeniaca, D. dahli, D. uzzelli and D. rostombekowi dated back to ~0.5 or ~0.9 Mya, depending on the calibration point used, while (2) D. bendimahiensis, D. sapphirina and D. unisexualis appear to have diverged ~1 or ~2 Mya.
Bi-allelic variants inCHKAcause a neurodevelopmental disorder with epilepsy and microcephaly
Authors: Klöckner Chiara , Fernández-Murray J Pedro , Tavasoli Mahtab , Sticht Heinrich , Stoltenburg-Didinger Gisela , Scholle Leila Motlagh , Bakhtiari Somayeh , Kruer Michael C , Darvish Hossein , Firouzabadi Saghar Ghasemi , Pagnozzi Alex , Shukla Anju , Girisha Katta Mohan , Narayanan Dhanya Lakshmi , Kaur Parneet , Maroofian Reza , Zaki Maha S , Noureldeen Mahmoud M , Merkenschlager Andreas , Gburek-Augustat Janina , Cali Elisa , Banu Selina , Nahar Kamrun , Efthymiou Stephanie , Houlden Henry , Jamra Rami Abou , Williams Jason , McMaster Christopher R , Platzer Konrad
Published: February 2022

The Kennedy pathways catalyse the de novo synthesis of phosphatidylcholine and phosphatidylethanolamine, the most abundant components of eukaryotic cell membranes. In recent years, these pathways have moved into clinical focus because four of ten genes involved have been associated with a range of autosomal recessive rare diseases such as a neurodevelopmental disorder with muscular dystrophy (CHKB), bone abnormalities and cone-rod dystrophy (PCYT1A) and spastic paraplegia (PCYT2, SELENOI).

We identified six individuals from five families with bi-allelic variants in CHKA presenting with severe global developmental delay, epilepsy, movement disorders and microcephaly. Using structural molecular modelling and functional testing of the variants in a cell-based Saccharomyces cerevisiae model, we determined that these variants reduce the enzymatic activity of CHKA and confer a significant impairment of the first enzymatic step of the Kennedy pathway.

In summary, we present CHKA as a novel autosomal recessive gene for a neurodevelopmental disorder with epilepsy and microcephaly.
Paediatric intracranial dural arteriovenous shunts: types, clinical presentation and therapeutic management
Authors: Smajda Stanislas J. , Söderman Michael , Dorfmüller Georg , Dorison Nathalie , Nghe Marie-Claire , Rodesch Georges L.
Published: February 2022

Paediatric intracranial dural arteriovenous shunts have clinical presentations and evolutions, with angiographic characteristics that differ from those described in adults. We report our experience concerning their therapeutic management, emphasizing the relevance of early diagnosis and appropriate treatment for satisfactory neurocognitive development. Using a prospective database, we reviewed the clinical and radiological data of all children with dural arteriovenous shunts managed between 2002 and 2020. Dural shunts were categorized into three types: dural sinus malformations with arteriovenous shunts; infantile dural arteriovenous shunts; and adult-type dural arteriovenous shunts. Therapeutic strategies and outcomes were analysed depending on lesional subtypes. Modified Rankin Scale for the paediatric population was assessed pre-treatment and at last follow-up. Twenty-eight patients [16 girls (57.1%); 12 boys (42.9%)] were included: 17 dural sinus malformation [10 boys (58.8%); seven girls (41.2%)], three infantile shunts [three girls (100%)], eight adult-type shunts [four girls (50%)]; four boys (50%)], with a mean age of 19.2 ± 36.6 months at presentation. Twelve (42.9%) had a modified Rankin Scale score of 0–2, four (14.3%) had a score of 3, three (10.7%) had a score of 4 and eight (28.6%) had a score of 5. Embolization was performed in 22 children [78.6%; 12 girls (54.5%); 10 boys (45.5%)]. Fifteen patients could be cured (68.2%): 11 dural sinus malformations (73.3%), four adult-type lesions (100%) but no infantile shunt. Mean post-treatment follow-up was 39.5 months (max. 139 months): 14 patients (63.6%) presented a modified Rankin Scale score of 0–2 and eight (36.4%) had a score ≥3. In the dural sinus malformation group, the modified Rankin Scale score was improved in 11 patients (73.3%) and unchanged in three (20%). Only one patient with infantile subtype (33.3%) improved clinically. In the adult-subtype group, all children (100%) improved. Of six untreated patients [four girls (66.7%); two boys (33.3%)], four with adult-subtype shunts showed uneventful evolutions, one with dural sinus malformation died, and therapeutic abortion was conducted in an antenatally diagnosed dural sinus malformation. Paediatric dural fistulas comprise different subtypes with variable clinical courses. Proper diagnosis is mandatory for optimal therapeutic strategies within appropriate therapeutic windows.
Tau propagation is dependent on the genetic background of mouse strains
Authors: Dujardin Simon , Fernandes Analiese , Bannon Riley , Commins Caitlin , De Los Santos Mark , Kamath Tarun V. , Hayashi Mansuo , Hyman Bradley T.
Published: February 2022

Progressive cognitive decline in Alzheimer’s disease correlates closely with the spread of tau protein aggregation across neural networks of the cortical mantle. We tested the hypothesis that heritable factors may influence the rate of propagation of tau pathology across brain regions in a model system, taking advantage of well-defined genetically diverse background strains in mice. We virally expressed human tau locally in the hippocampus and the entorhinal cortex neurons and monitored the cell-to-cell tau protein spread by immunolabelling. Interestingly, some strains showed more tau spreading than others while tau misfolding accumulated at the same rate in all tested mouse strains. Genetic factors may contribute to tau pathology progression across brain networks, which could help refine mechanisms underlying tau cell-to-cell transfer and accumulation, and potentially provide targets for understanding patient-to-patient variability in the rate of disease progression in Alzheimer’s disease.
Brain network topology early after stroke relates to recovery
Authors: Nemati Paul R. , Backhaus Winifried , Feldheim Jan , Bönstrup Marlene , Cheng Bastian , Thomalla Götz , Gerloff Christian , Schulz Robert
Published: February 2022

Analyses of alterations of brain networks have gained an increasing interest in stroke rehabilitation research. Compared with functional networks derived from resting-state analyses, there is limited knowledge of how structural network topology might undergo changes after stroke and, more importantly, if structural network information obtained early after stroke could enhance recovery models to infer later outcomes. The present work re-analysed cross-sectional structural imaging data, obtained within the first 2 weeks, of 45 acute stroke patients (22 females, 24 right-sided strokes, age 68 ± 13 years). Whole-brain tractography was performed to reconstruct structural connectomes and graph-theoretical analyses were employed to quantify global network organization with a focus on parameters of network integration and modular processing. Graph measures were compared between stroke patients and 34 healthy controls (15 females, aged 69 ± 10 years) and they were integrated with four clinical scores of the late subacute stage, covering neurological symptom burden (National Institutes of Health Stroke Scale), global disability (modified Rankin Scale), activity-related disability (Barthel Index) and motor functions (Upper-Extremity Score of the Fugl-Meyer Assessment). The analyses were employed across the complete cohort and, based on clustering analysis, separately within subgroups stratified in mild to moderate (n = 21) and severe (n = 24) initial deficits. The main findings were (i) a significant reduction of network’s global efficiency, specifically in patients with severe deficits compared with controls (P = 0.010) and (ii) a significant negative correlation of network efficiency with the extent of persistent functional deficits at follow-up after 3–6 months (P ≤ 0.032). Specifically, regression models revealed that this measure was capable to increase the explained variance in future deficits by 18% for the modified Rankin Scale, up to 24% for National Institutes of Health Stroke Scale, and 16% for Barthel Index when compared with models including the initial deficits and the lesion volume. Patients with mild to moderate deficits did not exhibit a similar impact of network efficiency on outcome inference. Clustering coefficient and modularity, measures of segregation and modular processing, did not exhibit comparable structure–outcome relationships, neither in severely nor in mildly affected patients. This study provides empirical evidence that structural network efficiency as a graph-theoretical marker of large-scale network topology, quantified early after stroke, relates to recovery. Notably, this contribution was only evident in severely but not mildly affected stroke patients. This suggests that the initial clinical deficit might shape the dependency of recovery on global network topology after stroke.
Flexible and Controllable Access Policy Update for Encrypted Data Sharing in the Cloud
Authors: Wang Ti , Zhou Yongbin , Ma Hui , Zhang Rui
Published: February 2022

As a promising service paradigm, cloud computing has attracted lots of enterprises and individuals to outsource big data to public cloud. To facilitate secure data using and sharing, ciphertext-policy attribute-based encryption (CP-ABE) is a suitable solution, which can provide fine-grained access control and encryption functionalities simultaneously. However, some serious challenges are still remaining toward achieving flexible and controllable access policy update in CP-ABE, which essentially impede the powerful access control ability of CP-ABE from long-term and large-scale deployment in real systems. In this work, we propose a novel scheme named policy updatable CP-ABE for encrypted data sharing scenes. The proposed scheme features the following achievements: (i) it supports fine-grained update algorithms with no restriction on update time; (ii) the cloud server can effectively verify update ciphertexts, so the integrity of original data would not be compromised intentionally or accidentally during the update and (iii) most operations of encryption and policy update are securely outsourced to cloud servers, leaving extremely low overheads for data owners and users. We formally define its security model and prove it is adaptively secure. Also, we implement the proposed scheme using the Charm framework. The experiment results demonstrate that it is efficient and practical.
Elevated Temperature Reduces Overwintering Survival of an Avian Ectoparasite, the Swallow Bug (Hemiptera: Cimicidae:Cimex vicarius)
Authors: Brown Charles R , Hannebaum Stacey L , Eaton-Clark Andrew , Booth Warren , O’Brien Valerie A
Published: February 2022

The survival of insects that are dormant in winter may either increase or decrease as a consequence of elevated winter temperatures under climate change. Warming can be deleterious when metabolism of the overwintering life stages increases to the point that energy reserves are exhausted before postoverwintering reemergence. We examined experimentally how overwintering survival of swallow bugs (Hemiptera: Cimicidae: Cimex vicarius Horvath), an ectoparasite primarily of cliff swallows (Passeriformes: Hirundinidae: Petrochelidon pyrrhonota Vieillot), was affected by a 3°C rise in mean daily temperature for populations in Oklahoma, Nebraska, and North Dakota. Adult and nymphal swallow bugs exposed to elevated temperature had an average reduction of approximately 31% in overwintering survival (from July/August to April/May), relative to controls exposed to current region-specific ambient-like conditions. Adult males in both groups survived less well in Nebraska and North Dakota than adult males in Oklahoma, but there was no consistent latitudinal effect of the elevated heat treatment. Our results indicate that projected increases in mean temperature in the Great Plains by 2050 could result in fewer swallow bugs surviving the winter and thus a reduced population size upon the arrival of their primary host in the spring, potentially affecting cliff swallow reproductive success, site use, and breeding phenology. Global climate change may alter the dynamics of host–parasite systems by reducing overall parasite abundance.
A polygenic risk score improves risk stratification of coronary artery disease: a large-scale prospective Chinese cohort study
Authors: Lu Xiangfeng , Liu Zhongying , Cui Qingmei , Liu Fangchao , Li Jianxin , Niu Xiaoge , Shen Chong , Hu Dongsheng , Huang Keyong , Chen Jichun , Xing Xiaolong , Zhao Yingxin , Lu Fanghong , Liu Xiaoqing , Cao Jie , Chen Shufeng , Ma Hongxia , Yu Ling , Wu Xianping , Wu Xigui , Li Ying , Zhang Huan , Mo Xingbo , Zhao Liancheng , Huang Jianfeng , Wang Laiyuan , Wen Wanqing , Shu Xiao-Ou , Takeuchi Fumihiko , Koh Woon-Puay , Tai E Shyong , Cheng Ching-Yu , Wong Tien yin , Chang Xuling , Chan Mark Yan-Yee , Gao Wei , Zheng Hong , Chen Kexin , Chen Jing , He Jiang , Tang Clara Sze-man , Lam Karen Siu Ling , Tse Hung-fat , Cheung Chloe Yu Yan , Takahashi Atsushi , Kubo Michiaki , Kato Norihiro , Terao Chikashi , Kamatani Yoichiro , Sham Pak Chung , Heng Chew-Kiat , Hu Zhibin , Chen Y Eugene , Wu Tangchun , Shen Hongbing , Willer Cristen J , Gu Dongfeng
Published: February 2022

Aims

To construct a polygenic risk score (PRS) for coronary artery disease (CAD) and comprehensively evaluate its potential in clinical utility for primary prevention in Chinese populations.

Methods and results

Using meta-analytic approach and large genome-wide association results for CAD and CAD-related traits in East Asians, a PRS comprising 540 genetic variants was developed in a training set of 2800 patients with CAD and 2055 controls, and was further assessed for risk stratification for CAD integrating with the guideline-recommended clinical risk score in large prospective cohorts comprising 41 271 individuals. During a mean follow-up of 13.0 years, 1303 incident CAD cases were identified. Individuals with high PRS (the highest 20%) had about three-fold higher risk of CAD than the lowest 20% (hazard ratio 2.91, 95% confidence interval 2.43–3.49), with the lifetime risk of 15.9 and 5.8%, respectively. The addition of PRS to the clinical risk score yielded a modest yet significant improvement in C-statistic (1%) and net reclassification improvement (3.5%). We observed significant gradients in both 10-year and lifetime risk of CAD according to the PRS within each clinical risk strata. Particularly, when integrating high PRS, intermediate clinical risk individuals with uncertain clinical decision for intervention would reach the risk levels (10-year of 4.6 vs. 4.8%, lifetime of 17.9 vs. 16.6%) of high clinical risk individuals with intermediate (20–80%) PRS.

Conclusion

The PRS could stratify individuals into different trajectories of CAD risk, and further refine risk stratification for CAD within each clinical risk strata, demonstrating a great potential to identify high-risk individuals for targeted intervention in clinical utility.