bluuebunny/crossref_metadata_2025_split huggingface dataset:
A nationwide population-based study on the clinical and economic burden of anastomotic leakage in colorectal surgery
Authors: Weber Marie-Christin , Berlet Maximilian , Stoess Christian , Reischl Stefan , Wilhelm Dirk , Friess Helmut , Neumann Philipp-Alexander 
Published: January 2023

Abstract

Aim
Anastomotic leakage (AL) is one of the most dreaded complications in colorectal surgery. In 2013, the International Classification of Diseases code K91.83 for AL was introduced in Germany, allowing nationwide analysis of AL rates and associated parameters. The aim of this population-based study was to investigate the current incidence, risk factors, mortality, clinical management, and associated costs of AL in colorectal surgery.

Methods
A data query was performed based on diagnosis-related group data of all hospital cases of inpatients undergoing colon or sphincter-preserving rectal resections between 2013 and 2018 in Germany.

Results
A total number of 690,690 inpatient cases were included in this study. AL rates were 6.7% for colon resections and 9.2% for rectal resections in 2018. Regarding the treatment of AL, the application of endoluminal vacuum therapy increased during the studied period, while rates of relaparotomy, abdominal vacuum therapy, and terminal enterostomy remained stable. AL was associated with significantly increased in-house mortality (7.11% vs. 20.11% for colon resections and 3.52% vs. 11.33% for rectal resections in 2018) and higher socioeconomic costs (mean hospital reimbursement volume per case: 14,877€ (no AL) vs. 37,521€ (AL) for colon resections and 14,602€ (no AL) vs. 30,606€ (AL) for rectal resections in 2018).

Conclusions
During the studied time period, AL rates did not decrease, and associated mortality remained at a high level. Our study provides updated population-based data on the clinical and economic burden of AL in Germany. Focused research in the field of AL is still urgently necessary to develop targeted strategies to prevent AL, improve patient care, and decrease socioeconomic costs.
Evolving shallow conduit revealed by tremor and vent activity observations during episodic lava fountaining of the 2021 Geldingadalir eruption, Iceland
Authors: Eibl Eva P. S. , Thordarson Thor , Höskuldsson Ármann , Gudnason Egill Á. , Dietrich Thoralf , Hersir Gylfi Páll , Ágústsdóttir Thorbjörg 
Published: January 2023

AbstractCyclic behaviour is observed in volcanic phenomena ranging from caldera collapses to explosions, spattering or lava fountaining. The repeating processes can define irregular, regular or systematically changing patterns. These patterns yield information about the subsurface structure, which often is not considered in detail. We analyse the pattern of 7058 lava fountaining episodes that occur between 2 May and 14 June 2021 during the Geldingadalir eruption, Iceland. Our seismometer records the lava fountaining episodes as tremor episodes. We analyse the seismic tremor amplitude, the episode duration, the repose time and the sum of episode duration and repose time (cycle duration). We define six periods characterised by different patterns: Three periods feature long episodes that exponentially shorten with time. One period features coexisting long and short episodes in a haphazard sequence. One period shows a stable pulsing duration but increasing repose time, and one period has stable, short episodes and repose times. We conclude that the episodic fountaining starts because a shallow-conduit container forms on 2 May shifting the magma degassing from sustained continuous to an episodic state. This situation evolves until 11 May when a semi-stable state is reached. The length of the repose times is most likely influenced by the amount of outgassed magma present in the uppermost part of the shallow conduit. Finally, we suggest that the vent is mechanically eroded and widens with time causing increasing seismic tremor amplitudes. However, the trends are frequently punctuated by partial crater wall collapses that temporarily disrupt the system.
Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee
Authors: Turner Dann , Shkoporov Andrey N. , Lood Cédric , Millard Andrew D. , Dutilh Bas E. , Alfenas-Zerbini Poliane , van Zyl Leonardo J. , Aziz Ramy K. , Oksanen Hanna M. , Poranen Minna M. , Kropinski Andrew M. , Barylski Jakub , Brister J Rodney , Chanisvili Nina , Edwards Rob A. , Enault François , Gillis Annika , Knezevic Petar , Krupovic Mart , Kurtböke Ipek , Kushkina Alla , Lavigne Rob , Lehman Susan , Lobocka Malgorzata , Moraru Cristina , Moreno Switt Andrea , Morozova Vera , Nakavuma Jesca , Reyes Muñoz Alejandro , Rūmnieks Jānis , Sarkar BL , Sullivan Matthew B. , Uchiyama Jumpei , Wittmann Johannes , Yigang Tong , Adriaenssens Evelien M. 
Published: January 2023

AbstractThis article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
A survey on deep learning approaches for text-to-SQL
Authors: Katsogiannis-Meimarakis George , Koutrika Georgia 
Published: January 2023

AbstractTo bridge the gap between users and data, numerous text-to-SQL systems have been developed that allow users to pose natural language questions over relational databases. Recently, novel text-to-SQL systems are adopting deep learning methods with very promising results. At the same time, several challenges remain open making this area an active and flourishing field of research and development. To make real progress in building text-to-SQL systems, we need to de-mystify what has been done, understand how and when each approach can be used, and, finally, identify the research challenges ahead of us. The purpose of this survey is to present a detailed taxonomy of neural text-to-SQL systems that will enable a deeper study of all the parts of such a system. This taxonomy will allow us to make a better comparison between different approaches, as well as highlight specific challenges in each step of the process, thus enabling researchers to better strategise their quest towards the “holy grail” of database accessibility.
Softmax policy gradient methods can take exponential time to converge
Authors: Li Gen , Wei Yuting , Chi Yuejie , Chen Yuxin 
Published: January 2023

AbstractThe softmax policy gradient (PG) method, which performs gradient ascent under softmax policy parameterization, is arguably one of the de facto implementations of policy optimization in modern reinforcement learning. For$$\gamma $$γ-discounted infinite-horizon tabular Markov decision processes (MDPs), remarkable progress has recently been achieved towards establishing global convergence of softmax PG methods in finding a near-optimal policy. However, prior results fall short of delineating clear dependencies of convergence rates on salient parameters such as the cardinality of the state space$${\mathcal {S}}$$Sand the effective horizon$$\frac{1}{1-\gamma }$$11-γ, both of which could be excessively large. In this paper, we deliver a pessimistic message regarding the iteration complexity of softmax PG methods, despite assuming access to exact gradient computation. Specifically, we demonstrate that the softmax PG method with stepsize$$\eta $$ηcan take$$\begin{aligned} \frac{1}{\eta } |{\mathcal {S}}|^{2^{\Omega \big (\frac{1}{1-\gamma }\big )}} ~\text {iterations} \end{aligned}$$1η|S|2Ω(11-γ)iterationsto converge, even in the presence of a benign policy initialization and an initial state distribution amenable to exploration (so that the distribution mismatch coefficient is not exceedingly large). This is accomplished by characterizing the algorithmic dynamics over a carefully-constructed MDP containing only three actions. Our exponential lower bound hints at the necessity of carefully adjusting update rules or enforcing proper regularization in accelerating PG methods.
Balancing disturbance risk and ecosystem service provisioning in Swiss mountain forests: an increasing challenge under climate change
Authors: Thrippleton Timothy , Temperli Christian , Krumm Frank , Mey Reinhard , Zell Jürgen , Stroheker Sophie , Gossner Martin M. , Bebi Peter , Thürig Esther , Schweier Janine 
Published: January 2023

AbstractClimate change severely affects mountain forests and their ecosystem services, e.g., by altering disturbance regimes. Increasing timber harvest (INC) via a close-to-nature forestry may offer a mitigation strategy to reduce disturbance predisposition. However, little is known about the efficiency of this strategy at the scale of forest enterprises and potential trade-offs with biodiversity and ecosystem services (BES). We applied a decision support system which accounts for disturbance predisposition and BES indicators to evaluate the effect of different harvest intensities and climate change scenarios on windthrow and bark beetle predisposition in a mountain forest enterprise in Switzerland. Simulations were carried out from 2010 to 2100 under historic climate and climate change scenarios (RCP4.5, RCP8.5). In terms of BES, biodiversity (structural and tree species diversity, deadwood amount) as well as timber production, recreation (visual attractiveness), carbon sequestration, and protection against gravitational hazards (rockfall, avalanche and landslides) were assessed. The INC strategy reduced disturbance predisposition to windthrow and bark beetles. However, the mitigation potential for bark beetle disturbance was relatively small (− 2.4%) compared to the opposite effect of climate change (+ 14% for RCP8.5). Besides, the INC strategy increased the share of broadleaved species and resulted in a synergy with recreation and timber production, and a trade-off with carbon sequestration and protection function. Our approach emphasized the disproportionally higher disturbance predisposition under the RCP8.5 climate change scenario, which may threaten currently unaffected mountain forests. Decision support systems accounting for climate change, disturbance predisposition, and BES can help coping with such complex planning situations.
Altered vitamin B12 metabolism in the central nervous system is associated with the modification of ribosomal gene expression: new insights from comparative RNA dataset analysis
Authors: Mathew Aimee Rachel , Cavallucci Virve , Fidaleo Marco 
Published: January 2023

AbstractRecent studies have confirmed the direct role of vitamin B12 (VitB12) in the central nervous system (CNS) homeostasis; nevertheless, the detailed mechanisms are poorly understood. By analyzing RNA-Seq and microarray datasets obtained from databanks, this study aims to identify possible basic mechanisms, related to the brain, involved in altering the gene expression under VitB12 deficiency mimicking conditions. The database inquiry returned datasets generated from distinctly heterogeneous experimental sets and considering the quality and relevance requirements, two datasets from mouse and one from rat models were selected. The analyses of individual datasets highlighted a change in ribosomal gene expression in VitB12 deficiency mimicking conditions within each system. Specifically, a divergent regulation was observed depending on the animal model: mice showed a down regulation of the ribosomal gene expression, while rats an upregulation. Interestingly, E2f1 was significantly upregulated under VitB12 deficiency mimicking conditions in the animal models, with a greater upregulation in rats. The rat model also revealed putative E2F1 Transcription Factor Binding Sites (TFBSs) in the promoter of the differently regulated genes involved in ribosomal gene expression. This suggested the possibility that E2F1, being greater expressed in rats, could activate the ribosomal genes having E2F1 TFBSs, thus giving a plausible explication to the divergent regulation observed in animal models. Despite the great diversity of the experimental sets used to generate the datasets considered, a common alteration of the ribosomes exists, thereby indicating a possible basic and conserved response to VitB12 deficiency. Moreover, these findings could provide new insights on E2F1 and its association with CNS homeostasis and VitB12 deficiency.
Graphical Abstract
Morphological and antioxidant responses of Nopalea cochenillifera cv. Maya (edible Opuntia sp. “Kasugai Saboten”) to chilling acclimatization
Authors: Kondo Ayumu , Ito Masashi , Takeda Yusaku , Kurahashi Yuka , Toh Shigeo , Funaguma Toru 
Published: January 2023

AbstractTo clarify the wintering ability of the cactus Nopalea cochenillifera cv. Maya (edible Opuntia sp., common name “Kasugai Saboten”), we investigated the effects of temperature and antioxidant capacity on chilling acclimatization. We analyzed the anatomy of cladode chlorenchyma tissue of plants exposed to light under chilling. We found that chilling acclimatization can be achieved by exposure to approximately 15 °C for 2 weeks and suggest that it is affected by whether or not antioxidant capacity can recover. The overwintering cacti had the thinnest cuticle but firm cuticular wax, which is important in the acquisition of low temperature tolerance under strong light. In cacti with severe chilling injury, round swollen nuclei with clumping chloroplasts were localized in the upper part (axial side) of the cell, as though pushed up by large vacuoles in the lower part. In overwintering cacti, chloroplasts were arranged on the lateral side of the cell as in control plants, but they formed pockets: invaginations with a thin layer of chloroplast stroma that surrounded mitochondria and peroxisomes. Specific cellular structural changes depended on the degree of chilling stress and provide useful insights linking chloroplast behavior and structural changes to the environmental stress response.
Route effects in city-based survey knowledge estimates
Authors: Krukar Jakub , Navas Medrano Samuel , Schwering Angela 
Published: January 2023

AbstractWhen studying wayfinding in urban environments, researchers are often interested in obtaining measures of participants’ survey knowledge, i.e., their estimate of distant locations relative to other places. Previous work showed that distance estimations are consistently biased when no direct route is available to the queried target or when participants follow a detour. Here we investigated whether a corresponding bias is manifested in two other popular measures of survey knowledge: a pointing task and a sketchmapping task. The aim of this study was to investigate whether there is a systematic bias in pointing/sketchmapping performance associated with the preferred route choice in an applied urban setting. The results were mixed. We found moderate evidence for the presence of a systematic bias, but only for a subset of urban locations. When two plausible routes to the target were available, survey knowledge estimates were significantly biased in the direction of the route chosen by the participant. When only one plausible route was available, we did not find a statistically significant pattern. The results may have methodological implications for spatial cognition studies in applied urban settings that might be obtaining systematically biased survey knowledge estimates at some urban locations. Researchers should be aware that the choice of urban locations from which pointing and sketchmapping are performed might systematically distort the results, in particular when two plausible but diverging routes to the target are visible from the location.
Speciation and historical migration pattern interaction: examples from P. nigra and P. sylvestris phylogeography
Authors: Naydenov Krassimir D. , Naydenov Michel K. , Alexandrov Alexander , Gurov Todor , Gyuleva Veselka , Hinkov Georgi , Ivanovska Sofiya , Tsarev Anatoly , Nikolic Biljana , Goudiaby Venceslas , Carcaillet Christopher , Volosyanchuk Roman , Bojovic Srdjan , Vasilevski Kole , Matevski Vlado , Peruzzi Lorenzo , Christou Andreas , Paitaridou Despina , Goia Irina , Kamary Salim , Gulcu Suleyman , Ture Cengiz , Bogunic Faruk 
Published: January 2023

AbstractHere, from macrophylogeographic mtDNA empirical data, we propose a scenario for the evolution and speciation of two important forest trees, European black pine and Scotch pine, and their multiple subspecies and varieties. Molecular clock simulations revealed thatINDELvariability in thePinusmitochondrial genome is relatively old, i.e., from the Pliocene-Miocene epoch, and related to historical tectonic continental fluctuations rather than to climate change at a large geographic scale. For conservation and management biodiversity program recommendations, special attention is given to the relationships between different speciation models, historical migration patterns, and differences between peripheral and central populations. Species evolution involves the mixing of different speciation modes, and every speciation mode has different effects on different DNA types (e.g., mitochondrial vs. chloroplast vs. nuclear DNA). The misbalance between the contributions of different meta-population census sizes vs. effective population sizes to asymmetric migration patterns is the result of different genotypes (and subphylogenetic lines) responding to selection pressure and adaptive evolution. We propose initial minimal size of conservation unit (between 3 and 5 ha) from central and marginal natural area of distribution for both species in the dynamic management system for practical forest genetic diversity management. The proposed physical sizes were determined by the effective population size, effective radius of seed distribution data, forest density age dynamics, succession pattern, natural selection pressing and species biology [R-17].
The methodological problem of unit roots: stationarity and its consequences in the context of the Tinbergen debate
Authors: Nasir Muhammad Ali , Morgan Jamie 
Published: January 2023

AbstractIn this paper we highlight an important yet often neglected issue that arises within the context of the broader set of concerns set out in Keynes’s seminal critique of Tinbergen’s early work in econometrics and that is the problem of “trend” in the dataset. We use the example of conforming data to achieve stationarity to solve a problem of unit roots to highlight that Keynes concerns with the “logical issues” regarding the “conditions which the economic material must satisfy” still gains little attention in theory and practice. There is a lot more discussion of the technical aspects of method than there is reflection on conditions that must be satisfied when methods are applied. Concomitantly, there is a tendency to respond to problems of method by applying fixes rather than addressing the underlying problem. We illustrate various facets of the argument using central bank policy targeting and using examples of differencing, co-integration and Bayesian applications.
Iron overload consequences for submerged plants stoichiometry, homeostasis and performance
Authors: Rybak Michał , Drzewiecka Kinga , Woźniak Magdalena , Öksüz Safa , Krueger Michał , Sobczyński Tadeusz , Ratajczak Izabela , Joniak Tomasz 
Published: January 2023

AbstractAccelerated lakes eutrophication is one of the greatest challenges nowadays. To counteract its negative effects, large-scale restoration treatments are carried out worldwide. However, research in this field is mainly focused on the process effectiveness and there is a scarcity of studies concerning the impact of restoration treatments on water organisms and ecosystem homeostatsis. Our microcosm study presents the effects of a phosphorus coagulant (iron [III] chloride) on functional traits changes, oxidative stress and macro- and microelement stoichiometry disturbances in macrophyte Myriophyllum spicatum, a model species inhabiting eutrophic waters. Application of the coagulant to experimental vessels influenced the physicochemical and optical parameters of water and led to significant changes in biogeochemistry. Stoichiometric alterations were reflected by disturbances in the relative contents of macro- (C, N, P, Ca, Mg) and microelements (Fe, Zn, Cu, Co) and induced luxury consumption of available ions. Physicochemical and stoichiometric changes mutually exerted negative influence on M. spicatum functional traits. The parameters of oxidative stress remained at low levels, comparable to the untreated control whereas stoichiometric analysis revealed the activation of mechanisms responsible for minimizing low light stress. The ability of M. spicatum to maintain homeostasis of Cu and Co under simulated chemical water restoration was closely related to high concentrations of Fe and Zn ions, which simultaneously were not subjected to homeostasis control. Thus, chemical lake restoration treatments based on phosphorus coagulants are not as environmentally safe as previously considered and may have far-reaching consequences for the biogeochemical cycle and food web functioning.
Automated opioid risk scores: a case for machine learning-induced epistemic injustice in healthcare
Authors: Pozzi Giorgia 
Published: January 2023

AbstractArtificial intelligence-based (AI) technologies such as machine learning (ML) systems are playing an increasingly relevant role in medicine and healthcare, bringing about novel ethical and epistemological issues that need to be timely addressed. Even though ethical questions connected to epistemic concerns have been at the center of the debate, it is going unnoticed how epistemic forms of injustice can be ML-induced, specifically in healthcare. I analyze the shortcomings of an ML system currently deployed in the USA to predict patients’ likelihood of opioid addiction and misuse (PDMP algorithmic platforms). Drawing on this analysis, I aim to show that the wrong inflicted on epistemic agents involved in and affected by these systems’ decision-making processes can be captured through the lenses of Miranda Fricker’s account of hermeneutical injustice. I further argue that ML-induced hermeneutical injustice is particularly harmful due to what I define as an automated hermeneutical appropriation from the side of the ML system. The latter occurs if the ML system establishes meanings and shared hermeneutical resources without allowing for human oversight, impairing understanding and communication practices among stakeholders involved in medical decision-making. Furthermore and very much crucially, an automated hermeneutical appropriation can be recognized if physicians are strongly limited in their possibilities to safeguard patients from ML-induced hermeneutical injustice. Overall, my paper should expand the analysis of ethical issues raised by ML systems that are to be considered epistemic in nature, thus contributing to bridging the gap between these two dimensions in the ongoing debate.