bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial and temporal distances in a virtual global world: Lessons from the COVID-19 pandemic
Authors: Nachum Lilac , Buckley Peter J. 
Published: December 2022

AbstractThe experience of COVID-19 prompted us to rethink the imperatives of distance for the organization of value-creating activities globally. We advance a conceptualization of distance as representing separation in both space and time and posit that these distance dimensions represent different kinds of separation and require varied theoretical attention. We delineate the intrinsic qualities of spatial and temporal distances and theorize the impact of this extended conceptualization of distance on major tenets of international business theory and their predictions regarding the patterns of international business activity. We illustrate the ways by which varying configurations of spatial and temporal distances serve different value-creating activities and draw their implications for countries’ global integration. We advance a call for more attention to time and temporal distance and their impact on the ways firms organize their value-creating activities in an increasingly virtual world.
Validity of three risk prediction models for dementia or cognitive impairment in Australia
Authors: Geethadevi Gopisankar M , Peel Roseanne , Bell J Simon , Cross Amanda J , Hancock Stephen , Ilomaki Jenni , Tang Titus , Attia John , George Johnson 
Published: December 2022

Abstract

Background
no studies have compared the predictive validity of different dementia risk prediction models in Australia.

Objectives
(i) to investigate the predictive validity of the Australian National University-Alzheimer’s Disease Risk Index (ANU-ADRI), LIfestyle for BRAin Health (LIBRA) Index and cardiovascular risk factors, ageing and dementia study (CAIDE) models for predicting probable dementia/cognitive impairment in an Australian cohort. (ii) To develop and assess the predictive validity of a new hybrid model combining variables from the three models.

Methods
the Hunter Community Study (HCS) included 3,306 adults aged 55–85 years with a median follow-up of 7.1 years. Probable dementia/cognitive impairment was defined using Admitted Patient Data Collection, dispensing of cholinesterase inhibitors or memantine, or a cognitive test. Model validity was assessed by calibration and discrimination. A hybrid model was developed using deep neural network analysis, a machine learning method.

Results
120 (3.6%) participants developed probable dementia/cognitive impairment. Mean calibration by ANU-ADRI, LIBRA, CAIDE and the hybrid model was 19, 0.5, 4.7 and 3.4%, respectively. The discrimination of the models was 0.65 (95% CI 0.60–0.70), 0.65 (95% CI 0.60–0.71), 0.54 (95% CI 0.49–0.58) and 0.80 (95% CI 0.78–0.83), respectively.

Conclusion
ANU-ADRI and LIBRA were better dementia prediction tools than CAIDE for identification of high-risk individuals in this cohort. ANU-ADRI overestimated and LIBRA underestimated the risk. The new hybrid model had a higher predictive performance than the other models but it needs to be validated independently in longitudinal studies.
Functional underpinnings of feedback-enhanced test-potentiated encoding
Authors: Ludowicy Petra , Czernochowski Daniela , Arnaez-Telleria Jaione , Gurunandan Kshipra , Lachmann Thomas , Paz-Alonso Pedro M 
Published: December 2022

Abstract
The testing effect describes the finding that retrieval practice enhances memory performance compared to restudy practice. Prior evidence demonstrates that this effect can be boosted by providing feedback after retrieval attempts (i.e. test-potentiated encoding [TPE]). The present fMRI study investigated the neural processes during successful memory retrieval underlying this beneficial effect of correct answer feedback compared with restudy and whether additional performance feedback leads to further benefits. Twenty-seven participants learned cue-target pairs by (i) restudying, (ii) standard TPE including a restudy opportunity, or (iii) TPE including a restudy opportunity immediately after a positive or negative performance feedback. One day later, a cued retrieval recognition test was performed inside the MRI scanner. Behavioral results confirmed the testing effect and that adding explicit performance feedback-enhanced memory relative to restudy and standard TPE. Stronger functional engagement while retrieving items previously restudied was found in lateral prefrontal cortex and superior parietal lobe. By contrast, lateral temporo-parietal areas were more strongly recruited while retrieving items previously tested. Performance feedback increased the hippocampal activation and resulted in stronger functional coupling between hippocampus, supramarginal gyrus, and ventral striatum with lateral temporo-parietal cortex. Our results unveil the main functional dynamics and connectivity nodes underlying memory benefits from additional performance feedback.
No evidence of theory of mind reasoning in the human language network
Authors: Shain Cory , Paunov Alexander , Chen Xuanyi , Lipkin Benjamin , Fedorenko Evelina 
Published: December 2022

Abstract
Language comprehension and the ability to infer others’ thoughts (theory of mind [ToM]) are interrelated during development and language use. However, neural evidence that bears on the relationship between language and ToM mechanisms is mixed. Although robust dissociations have been reported in brain disorders, brain activations for contrasts that target language and ToM bear similarities, and some have reported overlap. We take another look at the language-ToM relationship by evaluating the response of the language network, as measured with fMRI, to verbal and nonverbal ToM across 151 participants. Individual-participant analyses reveal that all core language regions respond more strongly when participants read vignettes about false beliefs compared to the control vignettes. However, we show that these differences are largely due to linguistic confounds, and no such effects appear in a nonverbal ToM task. These results argue against cognitive and neural overlap between language processing and ToM. In exploratory analyses, we find responses to social processing in the “periphery” of the language network—right-hemisphere homotopes of core language areas and areas in bilateral angular gyri—but these responses are not selectively ToM-related and may reflect general visual semantic processing.
An agency perspective of regional economic resilience during COVID-19: the role of the local state’s place-based leadership in Kunshan, China
Authors: Wu Di , Hu Xiaohui , Chen Wen , Yuan Feng 
Published: December 2022

AbstractThrough a case study of Kunshan, China, this paper shows how a local state utilised place-based leadership to enhance regional economic resilience under the COVID-19 pandemic crisis. It unpacks how Kunshan effectively mitigated early economic disturbances induced by the COVID-19 pandemic, by two ways of leadership actions, namely, enacting jurisdictional power (that is formal leadership), and mobilising wide official and interpersonal networks (that is network leadership). Four specific local-state-led adaptive resilience processes or strategies are identified: stabilising labour supply, mitigating supply-chain disruptions, alleviating financial strains and reconfiguring market orientations. Through these proactive endeavours, the local state played an enabling role in aligning diverse stakeholders and resources across places, scales and sectors, thereby allaying economic shocks and enhancing regional economic resilience. This study contributes to the resilience literature by developing an agency-centric perspective to understanding regional economic resilience during the COVID-19 pandemic.
A rare gastric metastasis secondary to residual cystic duct carcinoma: case report and literature review
Authors: Qian Leimin , Huang Jianming 
Published: December 2022

AbstractAn unusual gastric metastasis from residual cystic duct carcinoma was reported, which was easily mistaken as primary gastric carcinoma before the surgery. A 50-year-old Chinese man presented with right upper abdominal discomfort. Based on the biopsy and computed tomography results, an advanced gastric antrum adenocarcinoma was primarily diagnosed. Intraoperatively, there were other findings: residual cystic duct with chronic hyperplasia, a suspected purulent cavity filled with grayish-brown cloudy liquid at the distal end of the cystic duct and the gallbladder socket. The patient underwent radical operation. Histopathological findings finally suggested that adenocarcinoma of the residual cystic duct infiltrated into the whole layer of the gastric wall. Postoperative adjuvant chemotherapy and immunotherapy were administered. The patient has achieved 20-month recurrence-free survival. The comprehensive treatment including radical surgery, adjuvant chemotherapy and immunotherapy may improve the prognosis of such patients.
Primary adenocarcinoma of an ileostomy in a Crohn patient: a case report
Authors: De Deken Julie , Stavrou Gregor A 
Published: December 2022

Abstract
Proctocolectomy with ileostomy is an established surgical treatment in patients with inflammatory bowel disease. Adenocarcinoma of an ileostomy is a rare complication in long-term ileostomies. We present the case of a 69-year-old man who presented with bloody stools and a tumour at the ileostomy site 37 years after ileostomy formation. Biopsies confirmed the presence of an adenocarcinoma. Imaging did not show any metastases or advanced local infiltration. A resection of the ileostomy with a broad safety margin and reimplantation of a new Ileostomy was performed. At 18-month follow-up, there is no sign of recurrence. Ileostomy adenocarcinoma in a Crohn’s disease patient is rare with only four cases described in literature. An en-bloc resection and relocation of the ileostomy is the recommended treatment. Education of patients and healthcare professionals on this long-term ileostomy complication is vital for the early diagnosis and treatment.
Interpreting ALMA non-detections of JWST super-early galaxies
Authors: Kohandel M , Ferrara A , Pallottini A , Vallini L , Sommovigo L , Ziparo F 
Published: December 2022

ABSTRACT
Recent attempts to detect [O iii] 88$\, \mu$m emission from super-early (z &gt; 10) galaxy candidates observed by JWST have been unsuccessful. Non-detections can be either due to wrong photometric redshifts or to the faintness of the line in such early systems. By using zoom-in simulations, we show that if redshifts of these galaxies are confirmed, they are faint and mostly fall below the local metal-poor $\rm [O\, {\small III}]-SFR$ relation as a result of their low ionization parameter, Uion ≲ 10−3. Such low Uion values are found in galaxies that are in an early assembly stage, and whose stars are still embedded in high-density natal clouds. However, the most luminous galaxy in our sample ($\rm {log}[L_{\rm {[O\, {\small III}]}}/\mathrm{L}_\odot ] = 8.4$, Uion ≈ 0.1) could be detected by ALMA in only 2.8 h.
MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data
Authors: De Riso Giulia , Sarnataro Antonella , Scala Giovanni , Cuomo Mariella , Della Monica Rosa , Amente Stefano , Chiariotti Lorenzo , Miele Gennaro , Cocozza Sergio 
Published: December 2022

Abstract
DNA methylation is an epigenetic mark implicated in crucial biological processes. Most of the knowledge about DNA methylation is based on bulk experiments, in which DNA methylation of genomic regions is reported as average methylation. However, average methylation does not inform on how methylated cytosines are distributed in each single DNA molecule. Here, we propose Methylation Class (MC) profiling as a genome-wide approach to the study of DNA methylation heterogeneity from bulk bisulfite sequencing experiments. The proposed approach is built on the concept of MCs, groups of DNA molecules sharing the same number of methylated cytosines. The relative abundances of MCs from sequencing reads incorporates the information on the average methylation, and directly informs on the methylation level of each molecule. By applying our approach to publicly available bisulfite-sequencing datasets, we individuated cell-to-cell differences as the prevalent contributor to methylation heterogeneity. Moreover, we individuated signatures of loci undergoing imprinting and X-inactivation, and highlighted differences between the two processes. When applying MC profiling to compare different conditions, we identified methylation changes occurring in regions with almost constant average methylation. Altogether, our results indicate that MC profiling can provide useful insights on the epigenetic status and its evolution at multiple genomic regions.
Inter-layer and inter-subject variability of diurnal gene expression in human skin
Authors: del Olmo Marta , Spörl Florian , Korge Sandra , Jürchott Karsten , Felten Matthias , Grudziecki Astrid , de Zeeuw Jan , Nowozin Claudia , Reuter Hendrik , Blatt Thomas , Herzel Hanspeter , Kunz Dieter , Kramer Achim , Ananthasubramaniam Bharath 
Published: December 2022

Abstract
The skin is the largest human organ with a circadian clock that regulates its function. Although circadian rhythms in specific functions are known, rhythms in the proximal clock output, gene expression, in human skin have not been thoroughly explored. This work reports 24 h gene expression rhythms in two skin layers, epidermis and dermis, in a cohort of young, healthy adults, who maintained natural, regular sleep-wake schedules. 10% of the expressed genes showed such diurnal rhythms at the population level, of which only a third differed between the two layers. Amplitude and phases of diurnal gene expression varied more across subjects than layers, with amplitude being more variable than phases. Expression amplitudes in the epidermis were larger and more subject-variable, while they were smaller and more consistent in the dermis. Core clock gene expression was similar across layers at the population-level, but were heterogeneous in their variability across subjects. We also identified small sets of biomarkers for internal clock phase in each layer, which consisted of layer-specific non-core clock genes. This work provides a valuable resource to advance our understanding of human skin and presents a novel methodology to quantify sources of variability in human circadian rhythms.
Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein
Authors: Sedhom Jacklin , Kinser Jason , Solomon Lee A 
Published: December 2022

Abstract
Protein–DNA binding is of a great interest due to its importance in many biological processes. Previous studies have presented many factors responsible for the recognition and specificity, but understanding the minimal informational requirements for proteins that bind to multiple DNA-sites is still an understudied area of bioinformatics. Here we focus on the hydrogen bonds displayed by the target DNA in the major groove that take part in protein-binding. We show that analyses focused on the base pair identity may overlook key hydrogen bonds. We have developed an algorithm that converts a nucleotide sequence into an array of hydrogen bond donors and acceptors and methyl groups. It then aligns these non-covalent interaction arrays to identify what information is being maintained among multiple DNA sequences. For three different DNA-binding proteins, Lactose repressor, controller protein and λ-CI repressor, we uncovered the minimal pattern of hydrogen bonds that are common amongst all the binding sequences. Notably in the three proteins, key interacting hydrogen bonds are maintained despite nucleobase mutations in the corresponding binding sites. We believe this work will be useful for developing new DNA binding proteins and shed new light on evolutionary relationships.
The Party on Remote Ground: Disengaging and Disappearing?
Authors: McDonnell Duncan , Stanford Bartholomew 
Published: December 2022

Abstract
The party on the ground has traditionally enabled linkage with the party in office along with providing candidates, selectorates, and campaign volunteers. While this still occurs in cities, we do not know how party organisation changes have affected remote areas. To investigate, we examine two remote Australian electorates: the Barkly in the Northern Territory and the Kimberley in Western Australia. Based on interviews with grassroots members, representatives and officials, we conclude that, although parties still exert their traditional functions in some remote areas, in others they have disengaged, rendering membership less meaningful and weakening the chain of democratic legitimacy.
Determining the ecophysiological limits of a narrow niche tropical conifer tree (Podocarpus trinitensis)
Authors: Spiers Joshua A , Oatham Michael P , Rostant Luke V , Farrell Aidan D 
Published: December 2022

AbstractMany tropical species live close to their thermal limits within a narrow niche. Here, we investigate the ecophysiological limits of the tropical tree Podocarpus trinitensis, which is endemic to Trinidad and Tobago where most populations exist as isolated stands on hilltops. Five wild stands from a range of elevations were compared in the field with measurements of leaf temperature, canopy cover, stomatal conductance (gs), chlorophyll content and several chlorophyll fluorescence parameters. A parallel greenhouse experiment was used to acclimate seedlings to ‘CONTROL’ and ‘HEAT’ treatments (with mid-day air temperatures of 34.5 and 37 °C respectively), after which the above parameters were measured along with photosynthetic light and temperature response curves, leaf morphology and in vitro Fv/Fm thermostability.There was a positive association between improved physiological performance and elevation. In the high elevation sites, leaf temperatures were significantly lower while most of the physiological parameters were higher (gs, chlorophyll content, ɸ PSII, ETRmax and Isat90). In the greenhouse, HEAT and CONTROL plants were similar for most parameters, except leaf temperature (which was coupled with air temperature) and leaf mass per unit area (which was higher in HEAT plants). Temperature response curves showed an optimum temperature for photosynthesis of 30 ± 0.5 °C (TOpt) and in vitro Fv/Fm indicated a critical temperature of 47.4 ± 0.38 °C for HEAT and 48.2 ± 0.24 °C for CONTROL (T50), with no indication of heat acclimation. Podocarpus trinitensis was found to be shade tolerant. In the field, seedlings established under a close canopy (&gt;95% canopy cover) and had a low light saturation point (LCP). In the greenhouse, where more light was available, seedlings retained a low light compensation point, light saturation point (LSP) and maximum photosynthetic rate (Amax). The results suggest that P. trinitensis is moderately heat tolerant with the higher elevation sites being more habitable, but stands are also able to survive near sea level under a closed canopy. The narrow niche, along with the 30 ± 0.5 °C optimum temperature for photosynthesis and the lack of thermal plasticity in critical temperature, suggests that P. trinitensis has little room to acclimate to temperatures higher than those currently experienced.
Multisite Study of Optical Genome Mapping of Retrospective and Prospective Constitutional Disorder Cohorts
Authors: Broeckel Ulrich , Iqbal M. Anwar , Levy Brynn , Sahajpal Nikhil , Nagy Peter L. , Scharer Gunter , Bossler Aaron D. , Rodriguez Vanessa , Stence Aaron , Skinner Cindy , Skinner Steven A , Kolhe Ravindra , Stevenson Roger 
Published: December 2022

ABSTRACTSeveral medical societies including the American College of Medical Genetics and Genomics, the American Academy of Neurology, and the Association of Molecular Pathology recommend chromosomal microarray (CMA) as the first-tier test in the genetic work-up for individuals with neurodevelopmental disorders such as developmental delay and intellectual disability, autism spectrum disorder, as well as other disorders suspected to be of genetic etiology. Although CMA has significantly increased the diagnostic yield for these disorders, limitations in the technology preclude detection of certain structural variations in the genome and requires reflexing to other cytogenomic and molecular methods. Optical genome mapping (OGM) is a high-resolution technology that utilizes ultra-high molecular weight DNA, fluorescently labeled at a hexamer motif found throughout the genome, to create a barcode pattern, analogous to G-banded karyotyping, that can detect all classes of structural variations at very high resolution by comparison to a reference genome.A multisite study, partially published previously, with a total of n=1037 datapoints was conducted and showed 99.6% concordance between OGM and standard-of-care (SOC) testing for completed cases. The current phase of this study included cases from individuals with suspected genetic conditions referred for cytogenomic testing in a prospective postnatal cohort (79 cases with OGM and SOC results) and a retrospective postnatal cohort (262; same criteria). Among these cohorts were an autism spectrum disorder cohort (135) group with negative or uninformative results on previous testing (72). Prospective cases referred for CMA were included in this study as an unbiased comparison, OGM results show 100% concordance with variants of uncertain significance, pathogenic variants, and likely pathogenic variants reported by CMA other SOC and found reportable variants in an additional 10.1% of cases. Among the autism spectrum disorder cohort, OGM found reportable variants in an additional 14.8% of cases. Based on this demonstration of the analytic validity and clinical utility of OGM by this multi-site assessment, and considering clinical diagnostics often require iterative testing for detection and diagnosis in postnatal constitutional disorders, OGM should be considered as a first-tier test for neurodevelopmental disorders and/or suspicion of a genetic disease.
Avidity sequencing of whole genomes from retinal degeneration pedigrees identifies causal variants
Authors: Biswas Pooja , Villanueva Adda , Krajacich Benjamin J. , Moreno Juan , Zhao Junhua , Berry Anne Marie , Lazaro Danielle , Lajoie Bryan R. , Kruglyak Semyon , Ayyagari Radha 
Published: December 2022

AbstractWhole genome sequencing has been an effective tool in the discovery of variants that cause rare disease. In this study, we determined the suitability of a novel avidity sequencing approach for rare disease applications. We built a sample to results workflow, combining the novel sequencing technology with standard library preparation kits, analysis workflows, and interpretation tools. We applied the workflow to ten pedigrees with inherited retinal degeneration (IRD) phenotype. Candidate variants of interest identified through whole genome sequencing were further evaluated using segregation analysis. Mutations in known IRD genes were detected in five of the ten cases. Genes with identified high confidence variants associated with retinal degeneration includedPEX6, ABCA4, CERKL, MAK, andRDH12. Pending confirmatory clinical sequencing, we observed a 50% diagnostic yield, consistent with previously reported outcomes of IRD patient analysis. The study confirms that avidity sequencing is effective in detection of causal mutations when used for whole genome sequencing in rare disease applications.