bluuebunny/crossref_metadata_2025_split huggingface dataset:
Boundary element methods for the wave equation based on hierarchical matrices and adaptive cross approximation
Authors: Seibel Daniel 
Published: December 2021

AbstractTime-domain Boundary Element Methods (BEM) have been successfully used in acoustics, optics and elastodynamics to solve transient problems numerically. However, the storage requirements are immense, since the fully populated system matrices have to be computed for a large number of time steps or frequencies. In this article, we propose a new approximation scheme for the Convolution Quadrature Method powered BEM, which we apply to scattering problems governed by the wave equation. We use $${\mathscr {H}}^2$$

H

2

-matrix compression in the spatial domain and employ an adaptive cross approximation algorithm in the frequency domain. In this way, the storage and computational costs are reduced significantly, while the accuracy of the method is preserved.
Index appearance record with preorders
Authors: Křetínský Jan , Meggendorfer Tobias , Waldmann Clara , Weininger Maximilian 
Published: December 2021

AbstractTransforming $$\omega $$
ω
-automata into parity automata is traditionally done using appearance records. We present an efficient variant of this idea, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and show that our method produces significantly smaller automata than previous approaches.
Recent advances in terahertz imaging: 1999 to 2021
Authors: Castro-Camus Enrique , Koch Martin , Mittleman Daniel M. 
Published: December 2021

AbstractWe discuss the progress in the field of THz imaging based on time-domain spectroscopy during the last 20 years emphasizing several highlights. These include 3D mapping of the water distribution of plants, THz reflection imaging of samples with arbitrary shape, burn wound imaging and the early diagnosis of diabetic foot disease. These applications greatly benefit from the introduction of fibre-coupled THz time-domain system operated by rugged and portable femtosecond fibre-lasers. THz imaging is a versatile measurement method that has a plethora of practical applications and great promise for the future.
The accessory neural arch: development, morphology, and systematic distribution
Authors: Thieme Philipp , Moritz Timo 
Published: December 2021

AbstractThe accessory neural arch is an oddly distributed character present in several non-acanthomorph teleostean taxa. Its homology was often implied but never satisfyingly tested. In this study, we attended this pending problem. We analyzed the morphology, development, and systematic distribution of the accessory neural arch in teleosts. Using a comprehensive taxon sampling of cleared and stained specimens, we evaluated if the accessory neural arch fulfils existing homology criteria. We then combined these data with recent genetic phylogenies and ancestral character state estimation to reconstruct the evolutionary history of the accessory neural arch. While its gross morphology and development fit homology criteria, results from ancestral character state estimations suggest multiple independent evolutions within teleosts. Although the accessory neural arch cannot be homologous between several teleostean taxa, the concept of parallelism may explain the presence of such a similar character in a variety of non-acanthomorph teleostean taxa.
Embeddings from protein language models predict conservation and variant effects
Authors: Marquet Céline , Heinzinger Michael , Olenyi Tobias , Dallago Christian , Erckert Kyra , Bernhofer Michael , Nechaev Dmitrii , Rost Burkhard 
Published: December 2021

AbstractThe emergence of SARS-CoV-2 variants stressed the demand for tools allowing to interpret the effect of single amino acid variants (SAVs) on protein function. While Deep Mutational Scanning (DMS) sets continue to expand our understanding of the mutational landscape of single proteins, the results continue to challenge analyses. Protein Language Models (pLMs) use the latest deep learning (DL) algorithms to leverage growing databases of protein sequences. These methods learn to predict missing or masked amino acids from the context of entire sequence regions. Here, we used pLM representations (embeddings) to predict sequence conservation and SAV effects without multiple sequence alignments (MSAs). Embeddings alone predicted residue conservation almost as accurately from single sequences as ConSeq using MSAs (two-state Matthews Correlation Coefficient—MCC—for ProtT5 embeddings of 0.596 ± 0.006 vs. 0.608 ± 0.006 for ConSeq). Inputting the conservation prediction along with BLOSUM62 substitution scores and pLM mask reconstruction probabilities into a simplistic logistic regression (LR) ensemble for Variant Effect Score Prediction without Alignments (VESPA) predicted SAV effect magnitude without any optimization on DMS data. Comparing predictions for a standard set of 39 DMS experiments to other methods (incl. ESM-1v, DeepSequence, and GEMME) revealed our approach as competitive with the state-of-the-art (SOTA) methods using MSA input. No method outperformed all others, neither consistently nor statistically significantly, independently of the performance measure applied (Spearman and Pearson correlation). Finally, we investigated binary effect predictions on DMS experiments for four human proteins. Overall, embedding-based methods have become competitive with methods relying on MSAs for SAV effect prediction at a fraction of the costs in computing/energy. Our method predicted SAV effects for the entire human proteome (~ 20 k proteins) within 40 min on one Nvidia Quadro RTX 8000. All methods and data sets are freely available for local and online execution through bioembeddings.com, https://github.com/Rostlab/VESPA, and PredictProtein.
Reducing complication rates for repeat craniotomies in glioma patients: a single-surgeon experience and comparison with the literature
Authors: Morshed Ramin A. , Young Jacob S. , Gogos Andrew J. , Haddad Alexander F. , McMahon James T. , Molinaro Annette M. , Sudhakar Vivek , Al-Adli Nadeem , Hervey-Jumper Shawn L. , Berger Mitchel S. 
Published: December 2021

Abstract
Background
There is a concern that glioma patients undergoing repeat craniotomies are more prone to complications. The study’s goal was to assess if the complication profiles for initial and repeat craniotomies were similar, to determine predictors of complications, and to compare results with those in the literature.

Methods
A retrospective study was conducted of glioma patients (WHO grade II–IV) who underwent either an initial or repeat craniotomy performed by the senior author from 2012 until 2019. Complications were recorded by discharge, 30 days, and 90 days postoperatively. New neurologic deficits were recorded by 90 days postoperatively. Multivariate regression was performed to identify factors associated with complications. A meta-analysis was performed to identify rates of complications based on number of prior craniotomies.

Results
Within the cohort of 714 patients, 400 (56%) had no prior craniotomies, 218 (30.5%) had undergone 1 prior craniotomy, and 96 (13.5%) had undergone ≥ 2 prior craniotomies. There were 27 surgical and 10 medical complications in 30 patients (4.2%) and 19 reoperations for complications in 19 patients (2.7%) with no deaths by 90 days. Complications, reoperation rates, and new neurologic deficits did not differ based on number of prior craniotomies. On multivariate analysis, older age (OR1.5, 95%CI 1.0–2.2) and significant leukocytosis due to steroid use (OR12.6, 95%CI 2.5–62.9) were predictors of complications. Complication rates in the cohort were lower than rates reported in the literature.

Conclusion
Contrary to prior reports in the literature, repeat craniotomies can be as safe as initial operations if surgeons implement best practices.
Waiting time for surgery influences the outcome in idiopathic normal pressure hydrocephalus — a population-based study
Authors: Chidiac Christine , Sundström N. , Tullberg M. , Arvidsson L. , Olivecrona M. 
Published: December 2021

Abstract

Introduction
Idiopathic normal pressure hydrocephalus (iNPH) is a disease that comes with a great impact on the patient’s life. The only treatment for iNPH, which is a progressive disease, is shunt surgery. It is previously indicated that early intervention might be of importance for the outcome.

Aim
To investigate if a longer waiting time for surgery, negatively influences the clinical outcome.

Methods
Eligible for this study were all iNPH patients (n = 3007) registered in the Swedish Hydrocephalus Quality Registry (SHQR) during 1st of January 2004–12th of June 2019. Waiting time, defined as time between the decision to accept a patient for surgery and shunt surgery, was divided into the intervals ≤ 3, 3.1–5.9 and ≥ 6 months. Clinical outcome was assessed 3 and 12 months after surgery using the modified iNPH scale, the Timed Up and Go (TUG) test and the mini mental state examination (MMSE).

Results
Three months after surgery, 57% of the patients with ≤ 3 months waiting time showed an improvement in modified iNPH scale (≥ 5 points) whereas 52% and 46% of patients with 3.1–5.9 and ≥ 6 months waiting time respectively improved (p = 0.0115). At 12 months of follow-up, the corresponding numbers were 61%, 52% and 51% respectively (p = 0.0536).

Conclusions
This population-based study showed that in patients with iNPH, shunt surgery should be performed within 3 months of decision to surgery, to attain the best outcome.
Attachment and mentalization as predictors of outcome in family therapy for adolescent anorexia nervosa
Authors: Jewell Tom , Herle Moritz , Serpell Lucy , Eivors Alison , Simic Mima , Fonagy Peter , Eisler Ivan 
Published: December 2021

AbstractAnorexia nervosa-focussed family therapy (FT-AN) is the first-line treatment for adolescent anorexia nervosa (AN), but the predictors of poor treatment response are not well understood. The main aim of this study was to investigate the role of attachment and mentalization in predicting treatment outcome. The secondary aims of the study were to investigate therapeutic alliance at 1 month as a predictor of outcome, and to test the associations between alliance and baseline attachment and mentalization. 192 adolescents with AN and their parents were recruited as they began family therapy in out-patient specialist eating disorder services. Self-report measures of attachment, mentalization, and emotion regulation were completed at the start of treatment by adolescent patients and one of their parents. Self-reported alliance scores were collected at one month. Higher scores on the Certainty Scale of the Reflective Functioning Questionnaire, completed by parents, which indicate over-certainty about mental states, were the strongest predictor of poor outcome (Odds Ratio: 0.42, CI: 0.20–0.87). Similarly, for adolescents, higher Lack of Clarity scores on the Difficulties in Emotion Regulation Scale, representing being unclear about one’s feelings, were predictive of positive treatment outcome (OR: 1.10, CI: 1.00–1.21). Higher alliance scores at 1 month predicted positive outcome, and were associated with attachment security and mentalization. These novel findings suggest that, particularly in parents, a tendency towards excessive certainty about mental states in others may predict poor outcome in FT-AN. Further research is warranted to replicate the finding and characterise families at risk of poor outcome.
Creating a common priority vector in intuitionistic fuzzy AHP: a comparison of entropy-based and distance-based models
Authors: Duleba Szabolcs , Alkharabsheh Ahmad , Gündoğdu Fatma Kutlu 
Published: December 2021

AbstractIn the case of conflicting individuals or evaluator groups, finding the common preferences of the participants is a challenging task. This statement also refers to Intuitionistic Fuzzy Analytic Hierarchy Process models, in which uncertainty of the scoring of individuals is well-handled, however, the aggregation of the modified scores is generally conducted by the conventional way of multi-criteria decision-making. This paper offers two options for this aggregation: the relatively well-known entropy-based, and the lately emerged distance-based aggregations. The manuscript can be considered as a pioneer work by analyzing the nature of distance-based aggregation under a fuzzy environment. In the proposed model, three clearly separable conflicting groups are examined, and the objective is to find their common priority vector, which can be satisfactory to all participant clusters. We have tested the model results on a real-world case study, on a public transport development decision-making problem by conducting a large-scale survey involving three different stakeholder groups of transportation. The comparison of the different approaches has shown that both entropy-based and distance-based techniques can provide a feasible solution based on their high similarity in the final ordinal and cardinal outcomes.
Behavior of structural lightweight concrete produced with expanded clay aggregate and after exposure to high temperatures
Authors: Nemes Rita , Abed Mohammed A. , Seyam Ahmed M. , Lublóy Éva 
Published: December 2021

AbstractThe residual compressive strength of eight lightweight concrete mixtures containing three commercial grading (Liapor HD 5 N, Liapor HD 7 N, and Liapor 8F) of coarse lightweight aggregate (LWA) were determined after to expose at high temperatures. Eight mixes were produced, two by normal weight aggregate and the rest by different types of LWA. The produced concrete was analyzed after high temperature exposure and the effect of using LWA, the type of LWA, and compaction method was studied. To do so, visual inspection, residual compressive strength, crack pattern, spalling, and thermoanalytical analysis were conducted. Generally, it could be concluded that concrete formulations with LWA behave more advantageous up to 500 °C, compared to those with quartz gravel aggregates. Moreover, this study found that an ideal type of LWA to produce structural concrete was Liapor HD 5 N, which was used for producing the mixes L1 and L3.
Structural analysis and seismic stratigraphy for delineation of Neoproterozoic-Cambrian petroleum system in central and eastern part of Bikaner–Nagaur basin, India
Authors: Mandal Anita , Saha Debasish , Kumar Asit 
Published: December 2021

AbstractBikaner–Nagaur basin is located in the northwestern part of India and lies on the rising flank of Punjab platform of Middle Indus basin in Pakistan. Existence of Neoproterozoic-Cambrian petroleum system was confirmed by the exploration activities in the western periphery of the basin, whereas vast areas of central and eastern parts remain unexplored. Knowledge of petroleum system in this unexplored part of the basin is limited due to non-availability of data. Recently, 2525 line km of regional 2D seismic data acquired for the first time by Government of India under National Seismic Program (NSP) unlocks the opportunity for comprehensive understanding of subsurface geology in unexplored part of the basin. Present work aims to interpret recently acquired 2D seismic data and integrate with available surface (outcrop) data, gravity and well data (drilled in western part of basin) for unfolding the petroleum system elements, structural configurations and stratigraphic features in the hitherto central-eastern part of the basin. Two Neoproterozoic-Cambrian hydrocarbon plays: (1) Jodhpur and (2) overlying Bilara/Hanseran Evaporite Group (HEG) were envisaged. Both the plays depicted distinctive seismic characteristics, structural alignment and distribution of reservoir, source and seal. Fluvio-deltaic sandstone within Jodhpur group and shallow marine fractured dolomites within Bilara/HEG showed potential reservoir characteristics whereas organic rich laminated dolomites, stromatolites and argillaceous litho-units within Bilara/HEG group have been predicted as prospective source. The Halite layers within HEG group were considered as effective regional seals. Fault bounded anticlinal structures associated with Cambrian compression have been identified as the main entrapment for hydrocarbon accumulation. The basin witnessed long tectonostratigraphic history with two major compressional phases Structures formed by Cambrian compression are likely to be charged as the time of source maturity and peak expulsion was later, during early Mesozoic period. Overall, the study indicates new opportunities and potential accumulation of hydrocarbon in the unexplored part of the basin.
Ultrasensitive analysis of genetic instability related to chemical exposure
Authors: Domoradzki Tomasz , Grochowski Piotr , Jaśkiewicz Anna , Pająk Beata 
Published: December 2021

AbstractOur concerns have been raised about whether prolonged exposure to ammunition-related chemicals could correlate with genomic instability predisposing to lung carcinogenesis. The group of professional soldiers engaged in routine ammunition analysis and its explosive properties testing. To assess the presence of an innate genetic profile, DNA isolated from swabs was analyzed with LungCarta and HS Lung Panels and MassARRAY Analyzer 4 mass spectrometry. The presence of new somatic single nucleotide polymorphisms (SNPs) was detected with liquid biopsy technique and circulating cell-free DNA (ccfDNA) isolation, which was further analyzed with UltraSeek Lung Panel. Both genetic profiles obtained for each individual were compared. Genetic analysis revealed that in professional soldiers with long-term exposure to ammunition-related toxic chemicals, new SNPs in genes related to lung carcinogenesis are present. The preliminary data indicate that using modern molecular techniques could be a valuable tool for monitoring the genome instability in context of occupational risk of harmful volatile toxic compounds and improving personnel safety. The analyzed group will be further enlarged, and follow-up studies will be continued.
Diffusion tensor imaging in unclear intramedullary tumor-suspected lesions allows separating tumors from inflammation
Authors: Hohenhaus Marc , Merz Yorn , Klingler Jan-Helge , Scholz Christoph , Hubbe Ulrich , Beck Jürgen , Wolf Katharina , Egger Karl , Reisert Marco , Kremers Nico 
Published: December 2021

Abstract
Design
Prospective diagnostic study.

Objectives
Primary imaging-based diagnosis of spinal cord tumor-suspected lesions is often challenging. The identification of the definite entity is crucial for dedicated treatment and therefore reduction of morbidity. The aim of this trial was to investigate specific quantitative signal patterns to differentiate unclear intramedullary tumor-suspected lesions based on diffusion tensor imaging (DTI).

Setting
Medical Center - University of Freiburg, Germany.

Methods
Forty patients with an unclear tumor-suspected lesion of the spinal cord prospectively underwent DTI. Primary diagnosis was determined by histological or clinical work-up or remained indeterminate with follow-up. DTI metrics (FA/ADC) were evaluated at the central lesion area, lesion margin, edema, and normal spinal cord and compared between different diagnostic groups (ependymomas, other spinal cord tumors, inflammations).

Results
Mean DTI metrics for all spinal cord tumors (n = 18) showed significantly reduced FA and increased ADC values compared to inflammatory lesions (n = 8) at the lesion margin (p < 0.001, p = 0.001) and reduced FA at the central lesion area (p < 0.001). There were no significant differences comparing the neoplastic subgroups of ependymomas (n = 10) and other spinal cord tumors (n = 8), but remaining differences for both compared to the inflammation subgroup. We found significant higher ADC (p = 0.040) and a trend to decreased FA (p = 0.081) for ependymomas compared to inflammations at the edema.

Conclusion
Even if distinct differentiation of ependymomas from other spinal cord neoplasms was not possible based on quantitative DTI metrics, FA and ADC were feasible to separate inflammatory lesions. This may avoid unnecessary surgery in patients with unclear intramedullary tumor-suspected lesions.
Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction
Authors: Schiøler Henrik , Knudsen Torben , Brøndum Rasmus Froberg , Stoustrup Jakob , Bøgsted Martin 
Published: December 2021

AbstractWhen a virus spreads, it may mutate into, e.g., vaccine resistant or fast spreading lineages, as was the case for the Danish Cluster-5 mink variant (belonging to the B.1.1.298 lineage), the British B.1.1.7 lineage, and the South African B.1.351 lineage of the SARS-CoV-2 virus. A way to handle such spreads is through a containment strategy, where the population in the affected area is isolated until the spread has been stopped. Under such circumstances, it is important to monitor whether the mutated virus is extinct via massive testing for the virus sub-type. If successful, the strategy will lead to lower and lower numbers of the sub-type, and it will eventually die out. An important question is, for how long time one should wait to be sure the sub-type is extinct? We use a hidden Markov model for infection spread and an approximation of a two stage sampling scheme to infer the probability of extinction. The potential of the method is illustrated via a simulation study. Finally, the model is used to assess the Danish containment strategy when SARS-CoV-2 spread from mink to man during the summer of 2020, including the Cluster-5 sub-type. In order to avoid further spread and mink being a large animal virus reservoir, this situation led to the isolation of seven municipalities in the Northern part of the country, the culling of the entire Danish 17 million large mink population, and a bill to interim ban Danish mink production until the end of 2021.
Mobile energy‐to‐home integration: An adaption of mobility as a service in urban energy systems
Authors: Luo Fengji , Zhao Zehua , Rashidi Taha Hossein 
Published: December 2021

AbstractMobility as a Service (MaaS) represents a paradigm shift from personally owned transportation modes towards mobility provided as a service. Using electric vehicles (EVs) as a mobile energy storage media, this article presents a new application scenario of MaaS in urban energy systems, referring to as the mobile energy to home (ME2H) integration. An architectural design of the ME2H system is proposed in this study, which is cantered by a ridesharing‐like booking system. Through the booking system, a customer can appoint nearby on‐road EVs to come to plug in and temporarily supply energy to their site with an agreed price lower than purchasing energy from the external grid. The ME2H booking system then interfaces with the customer‐side home energy management system and the EV driver‐side trip planner. Based on the ME2H booking schedules, the two decision‐making systems plan the household appliance operations and travel paths for the ME2H service receiver (the customer) and provider (the EV driver), respectively. This study also investigates two representative scenarios to demonstrate the effectiveness of ME2H in urban energy systems.