bluuebunny/crossref_metadata_2025_split huggingface dataset:
Provable Limitations of Acquiring Meaning from Ungrounded Form: What Will Future Language Models Understand?
Authors: Merrill William , Goldberg Yoav , Schwartz Roy , Smith Noah A. 
Published: November 2021

AbstractLanguage models trained on billions of tokens have recently led to unprecedented results on many NLP tasks. This success raises the question of whether, in principle, a system can ever “understand” raw text without access to some form of grounding. We formally investigate the abilities of ungrounded systems to acquire meaning. Our analysis focuses on the role of “assertions”: textual contexts that provide indirect clues about the underlying semantics. We study whether assertions enable a system to emulate representations preserving semantic relations like equivalence. We find that assertions enable semantic emulation of languages that satisfy a strong notion of semantic transparency. However, for classes of languages where the same expression can take different values in different contexts, we show that emulation can become uncomputable. Finally, we discuss differences between our formal model and natural language, exploring how our results generalize to a modal setting and other semantic relations. Together, our results suggest that assertions in code or language do not provide sufficient signal to fully emulate semantic representations. We formalize ways in which ungrounded language models appear to be fundamentally limited in their ability to “understand”.
A new atypical splice mutation in PKD2 leading to autosomal dominant polycystic kidney disease in a Chinese family
Authors: Zhang Junlin , Wang Yiting , Zhao Yingwang , Liu Fang 
Published: November 2021

Abstract

Introduction:
Autosomal dominant polycystic kidney disease (ADPKD) is a very common hereditary renal disorder. Mutations in PKD1 and PKD2, identified as disease-causing genes, account for 85% and 15% of the ADPKD cases, respectively.

Methods:
In this study, the mutation analysis of polycystic kidney disease (PKD) genes was performed in a Chinese family with suspected ADPKD using targeted clinical exome sequencing (CES). The candidate pathogenic variants were further tested by using Sanger sequencing and validated for co-segregation. In addition, reverse transcription-polymerase chain reaction (RT-PCR) was performed to test for abnormal splicing and assess its potential pathogenicity.

Results:
A novel atypical splicing mutation that belongs to unclassified variants (UCVs), IVS6+5G>C, was identified in three family members by CES and was shown to co-segregate only with the affected individuals. The RT-PCR revealed the abnormal splicing of exon 6, which thus caused truncating mutation. These findings suggested that the atypical splice site alteration, IVS6+5G>C, in the PKD2 gene was the potential pathogenic mutation leading to ADPKD in this Chinese family.

Conclusion:
The data available in this study provided strong evidence that IVS6+5G>C is the potential pathogenic mutation for ADPKD. In addition, our findings emphasised the significance of functional analysis of UCVs and genotype–phenotype correlation in ADPKD.
Dengue virus infection among renal transplant recipients in Singapore: a 15-year, single-centre retrospective review
Authors: Tan Sophie Seine Xuan , Ho Quan Yao , Thangaraju Sobhana , Tan Thuan Tong , Kee Terence , Chung Shimin Jasmine 
Published: November 2021

Abstract

Introduction:
Dengue is a mosquito-borne viral infection endemic in Singapore. Its impact on renal transplantation is limited to small case series. We aimed to characterise the clinical presentation and outcomes of dengue infection among renal transplant recipients in Singapore.

Methods:
We conducted a 15-year retrospective review of dengue in renal transplant patients treated at Singapore General Hospital between January 2005 and October 2019. The diagnosis of dengue was made if there were a compatible clinical syndrome and a positive dengue diagnostic assay (dengue non-structural 1 antigen, immunoglobulin M or reverse transcriptase-polymerase chain reaction).

Results:
Of the 31 patients diagnosed with dengue, 18 (58.1%) were deceased donor recipients. The median age was 52 (interquartile range [IQR] 40–61) years; 16 (51.6%) were females. The median time to diagnosis was 99 (IQR 18–169) months from transplant. The most common clinical symptoms were fever (87.1%), myalgia (41.9%), gastrointestinal symptoms (38.7%) and headache (25.8%). Nineteen (61.3%) patients had dengue without warning signs, nine (29.0%) had dengue with warning signs, three (9.7%) had severe dengue and 30 (96.8%) were hospitalised. Seventeen (54.8%) patients had graft dysfunction, 16 (94.1%) of whom had recovery of graft function. One (3.2%) patient required dialysis and subsequently died. There were two cases of donor-derived infections (DDIs) with favourable outcomes.

Conclusion:
Our experience with dengue in renal transplant recipients is concordant with published data. Although graft dysfunction is common, it is often transient with favourable outcomes. Outpatient management may be considered for mild infections. Although dengue DDIs are uncommon, more stringent donor screening may be considered in endemic regions.
Attacking Punitive Retribution at Its Heart – A Restorative Justice Thrust
Authors: van Willigenburg Theo , Van der Borght Eduardus 
Published: November 2021

Abstract
Restorative justice, aimed at restoring human relations instead of just punishing offenders, is often defended with reference to biblical values like reconciliation, forgiveness, and mercy. Advocates of retributivism, which is the philosophy that underlies the practice of punishing perpetrators with the sole goal of inflicting hardship on them, regularly ridicule such defenses. In response we will not directly defend restorative justice, but critically inquire in the main theoretical arguments with which advocates of retributivism seek to rationalize their view. We point out the weaknesses of these arguments and why we believe that restorative procedures can do much better in serving the goals of (criminal) justice.
Reacting to the Decline of the West?
Authors: Didier Brice 
Published: November 2021

Abstract
This article discusses the European Union (EU)’s strategic adaptation to the relative decline of the United States (US)-led Western world order by introducing the concept of hedging: a strategy of concomitant engagement with the system leader and its competitors aiming to minimise the risks of confrontation with either of them. To grasp the EU’s shift towards strategic hedging, the article analyses the subsequent 2003 Security Strategy, 2008 Implementation Report, 2015 Strategic Review and ongoing 2016 Global Strategy, and then puts the latter’s core concepts of ‘principled pragmatism’ and ‘strategic autonomy’ into perspective vis-à-vis international developments since 2016, related to ‘America First’ and the Sino-American rivalry. The article ultimately argues that, confronted with global power diffusion but constrained by the preponderance of transatlanticism, hedging has become a primary strategic option for the EU to emancipate from the US without alienating it and to compensate for the waning of the Western world order.
ERA5-Derived Precipitation: Insights from Historical Rainfall Networks in Southern Africa
Authors: Terblanche Deon , Lynch Amanda , Chen Zihan , Sinclair Scott 
Published: November 2021

Abstract
Patterns of freshwater availability—its variability and distribution—are already shifting as a function of global climate change and climate variability. High-resolution global gridded reanalysis products present an important tool to understand the already observed changes and thereby improve future scenarios as the climate evolves. A historical 100-yr-long district rainfall dataset and a unique set of highly detailed rainfall data from the highveld of South Africa spanning a 10-yr period provide an opportunity to independently evaluate the European Centre for Medium-Range Weather Forecasts ERA5 reanalysis product. Evaluation is challenged by the episodic nature of significant rainfall events of southern Africa as well as differences in spatial and temporal resolution between model output and surface precipitation data. Here we present a convergent methodology spanning annual to event time scales and regional to gauge-level spatial scales to identify the characteristics of systematic biases in variability and amount of rain as well as timing of events. We find that ERA5 is consistently wetter than observed in ways that affect the timing of individual events while performing well on metrics associated with large-scale trends and seasonal variability. Errors are associated with both stratiform and convective rainfall types, but the timing of onset of convective rainfall is a challenge that is critical in this summer-rainfall-dominated region.

Significance Statement
High-resolution gridded datasets are invaluable tools for gaining improved understanding of historical rainfall variations under the influence of climate change. In addition, these datasets provide consistent information for purposes such as water resources management. Quantification of dataset biases provides important guidance for robust decision-making as well as for the development of future climate scenarios. However, rainfall is an especially challenging quantity to assess. With the increasing incidence of drought and flood, methods that independently validate this high-resolution gridded data are needed to ensure high-quality knowledge support. This study demonstrates an approach using convergent streams of evidence to assess the European Centre for Medium-Range Weather Forecasts gridded rainfall dataset with the purpose of better understanding the evolving characteristics of rainfall in southern Africa.
Rainfall Microphysics Influenced by Strong Wind during a Tornadic Storm
Authors: Bolek Abdullah , Testik Firat Y. 
Published: November 2021

Abstract
Rainfall microphysical characteristics including raindrop fall speed, axis ratio, and canting angle were measured through field observations by using a high-speed optical disdrometer (HOD) during and after tornadic severe storm passage. High and low wind and turbulence characteristics were observed during and after passage, respectively, which provided an opportunity to compare the effects of the different wind and turbulence characteristics on raindrop characteristics. During passage, 9.4% of the raindrops larger than 1.0 mm in volume equivalent diameter (D) were identified as subterminal, whereas only 0.5% of the raindrops of the same size were detected as subterminal after passage. Contrary to findings in literature, we could not find any distinct superterminal fall speed behavior for raindrops with D < 1.0 mm during or after passage. For raindrops with D > 2.0 mm, deviations of the axis ratio distribution from the predicted distribution for the equilibrium raindrops were observed, and the deviations during passage were larger than those after passage. The deviations of the axis ratio distributions from the predicted distributions for the equilibrium raindrops were also observed for midsized (1.0 < D < 2.0 mm) raindrops; however, these deviations during and after passage were of similar magnitude. The canting angle distribution for raindrops with D > 2.0 mm was found to have the mean value of approximately 0° both during and after passage and the standard deviation values of 24.7° during passage and 13.6° after passage. This study shows the clear influence of wind on various rainfall microphysical characteristics and documents the observed value ranges of these characteristics under strong wind that are of importance for a number of rainfall applications, including radar rainfall retrievals and rainfall modeling.
Forecast Skill for California Heavy Precipitation Periods from the High-Resolution Rapid Refresh Model and the Coupled Ocean–Atmosphere Mesoscale Prediction System
Authors: Dougherty Kevin J. , Horel John D. , Nachamkin Jason E. 
Published: November 2021

Abstract
Precipitation forecasts from the High-Resolution Rapid Refresh model (HRRR) of the National Centers for Environmental Prediction (NCEP) and the Navy’s Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS) are examined during heavy precipitation periods in California. Precipitation forecast discrepancies between the two models are examined during a recent heavy winter precipitation episode in California from 6 to 8 December 2019. The skill of initial 12-h precipitation forecasts is examined objectively from 1 December 2018 to 28 February 2019 from the HRRR, COAMPS, and NCEP’s North American Mesoscale Forecast System (NAM-3km). The HRRR exhibited lower seasonal biases and higher skill based on several metrics applied to a sample of 48 12-h periods during California’s second wettest winter season during the past 20 years. Overall, the NAM-3km and COAMPS exhibited a large wet bias over the interior mountain regions while the HRRR model indicated a dry bias along the northern coastal region. All models tended to underestimate precipitation along the coastal mountains of Northern California. To highlight the regional and localized nature of forecast skill, the fraction skill score (FSS) metric is applied across ranges of spatial scales and precipitation values. For the domain as a whole, the HRRR had higher precipitation forecast skill compared to the other two models, particularly within radial distances of 20–30 km and moderate (10–50 mm) precipitation totals. FSS computed locally highlights the HRRR’s overall higher skill as well as enhanced skill in the southern half of the state.
How Is COVID-19 Affected by Weather? Metaregression of 158 Studies and Recommendations for Best Practices in Future Research
Authors: Tan Ling , Schultz David M. 
Published: November 2021

AbstractBecause many viral respiratory diseases show seasonal cycles, weather conditions could affect the spread of coronavirus disease 2019 (COVID-19). Although many studies pursued this possible link early in the pandemic, their results were inconsistent. Here, we assembled 158 quantitative empirical studies examining the link between weather and COVID-19. A metaregression analysis was performed on their 4793 correlation coefficients to explain these inconsistent results. We found four principal findings. First, 80 of the 158 studies did not state the time lag between infection and reporting, rendering these studies ineffective in determining the weather–COVID-19 relationship. Second, the research outcomes depended on the statistical analysis methods employed in each study. Specifically, studies using correlation tests produced outcomes that were functions of the geographical locations of the data from the original studies, whereas studies using linear regression produced outcomes that were functions of the analyzed weather variables. Third, Asian countries had more positive associations for air temperature than other regions, possibly because the air temperature was undergoing its seasonal increase from winter to spring during the rapid outbreak of COVID-19 in these countries. Fourth, higher solar energy was associated with reduced COVID-19 spread, regardless of statistical analysis method and geographical location. These results help to interpret the inconsistent results and motivate recommendations for best practices in future research. These recommendations include calculating the effects of a time lag between the weather and COVID-19, using regression analysis models, considering nonlinear effects, increasing the time period considered in the analysis to encompass more variety of weather conditions and to increase sample size, and eliminating multicollinearity between weather variables.Significance StatementMany respiratory viruses have seasonal cycles, and COVID-19 may, too. Many studies have tried to determine the effects of weather on COVID-19, but results are often inconsistent. We try to understand this inconsistency through statistics. For example, half of the 158 studies we examined did not account for the time lag between infection and reporting a COVID-19 case, which would make these studies flawed. Other studies showed that more COVID-19 cases occurred at higher temperatures in Asian countries, likely because the season was changing from winter to spring as the pandemic spread. We conclude with recommendations for future studies to avoid these kinds of pitfalls and better inform decision-makers about how the pandemic will evolve in the future.
Percutaneous Versus Surgical Insertion of Peritoneal Dialysis Catheters: A Systematic Review and Meta-Analysis
Authors: Agarwal Anirudh , Whitlock Reid H. , Bamforth Ryan J. , Ferguson Thomas W. , Sabourin Jenna M. , Hu Qiming , Armstrong Sean , Rigatto Claudio , Tangri Navdeep , Dunsmore Sara , Komenda Paul 
Published: November 2021

Background: Home-based peritoneal dialysis (PD) is an alternative to facility-based hemodialysis and has lower costs and greater freedom for patients with kidney failure. For a patient to undergo PD, a safe and reliable method of accessing the peritoneum is needed. However, different catheter insertion techniques may affect patient health outcomes. Objective: To compare the risk of infectious and mechanical complications between surgical (open and laparoscopic) PD catheter insertion and percutaneous catheter insertion. Design: Systematic review and meta-analysis. Setting: We searched for observational studies and randomized controlled trials (RCTs) in CENTRAL, EMBASE, MEDLINE, PubMed, and SCOPUS from inception until June 2018. Data were extracted by 2 independent reviewers based on a preformed template. Patients: Adult (aged 18+) patients with kidney failure who underwent a PD catheter insertion procedure. Measurements: We analyzed leak, malfunction, and bleed as early complications (occurring within 1 month of catheter insertion). Infectious complications (exit-site infections, tunnel infections, and peritonitis) were presented as both early complications and with the longest duration of follow-up. Methods: Random effects meta-analyses with the generic inverse variance method to estimate pooled rate ratios and 95% confidence intervals. We quantified heterogeneity by using the I2 statistic for inconsistency and assessed heterogeneity using the χ2 test. Sensitivity analysis was performed by removing studies at high risk of bias as measured with the Newcastle-Ottawa Scale and the Cochrane Risk of Bias tool. Results: Twenty-four studies (22 observational, 2 RCTs) with 3108 patients and 3777 catheter insertions were selected. Data from 2 studies were unable to be extracted and were qualitatively assessed. In the remaining 22 studies, percutaneous insertion was associated with a lower risk of both exit-site infections (risk ratio [RR] = 0.36, 95% confidence interval [CI] = 0.24-0.53, I2 = 0%) and peritonitis (RR = 0.52, 95% CI = 0.36-0.77, I2 = 3%) within 1 month of the procedure. There was no difference in mechanical complication rates between the 2 techniques. Limitations: Lack of consistency in the time periods for the various outcomes reported, risk of bias concerns with respect to population comparability, and the inability to analyze individual component causes of primary nonfunction (catheter obstruction, catheter migration, and leak). Conclusions: Our meta-analysis suggests differences in early infectious complications in favor of percutaneous insertion and no significant differences in mechanical complications compared with surgical insertion. These findings have implications on the direction of PD programs in terms of maximizing operating room resources.
Fatigue Property of Additively Manufactured Ti-6Al-4V under Nonproportional Multiaxial Loading
Authors: Kimura Yuya , Ogawa Fumio , Itoh Takamoto 
Published: November 2021

AbstractThe low cycle fatigue strength properties of the additively manufactured Ti-6Al-4V alloy are experimentally investigated under proportional and nonproportional multiaxial loading. The fatigue tests were conducted using hollow cylinder specimens with and without heat treatments, at room temperature in air. Two fatigue tests were conducted: one for proportional loading and one for nonproportional loading. The proportional loading was represented by a push-pull strain path (PP) and the nonproportional loading by a circle strain path (CI). The failure lives of the additively manufactured specimens were clearly reduced drastically by internal voids and defects. However, the sizes of the defects were measured, and the defects were found not to cause a reduction in fatigue strength above a critical size. The fracture surface was observed using scanning electron microscopy to investigate the fracture mechanisms of the additively manufactured specimens under the two types of strain paths. Different fracture patterns were recognized for each strain paths; however, both showed retention of the crack propagation, despite the presence of numerous defects, probably because of the interaction of the defects. The crack propagation properties of the materials with numerous defects under nonproportional multiaxial loading were clarified to increase the reliability of the additively manufactured components.
Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar
Authors: Cheng Zihan , Zhang Xuemei , Yao Wenjing , Gao Yuan , Zhao Kai , Guo Qing , Zhou Boru , Jiang Tingbo 
Published: November 2021

Abstract
Background
Xyloglucan endotransglucosylase/hydrolase (XTH) family plays an important role in cell wall reconstruction and stress resistance in plants. However, the detailed characteristics of XTH family genes and their expression pattern under salt stress have not been reported in poplar.

Results
In this study, a total of 43 PtrXTH genes were identified from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoters of the PtrXTH genes contain mutiple cis-acting elements related to growth and development and stress responses. Collinearity analysis revealed that the XTH genes from poplar has an evolutionary relationship with other six species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Based on RNA-Seq analysis, the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, there are11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress. In addition, the accuracy of RNA-Seq results was verified by RT-qPCR.

Conclusion
All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study will lay a theoretical foundation for further study on molecular function of XTH genes in poplar.