bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards low carbon development strategies from forestry sector in West Papua
Authors: Hendri  , Raharjo Syarifudin , Suarga Egi , Faruk Rosyaridho M. , Kalmirah Julia
Published: February 2022

The forestry sector plays an important role in mitigating and adapting to climate change. In the NDC Indonesia Report (2021), forestry and other land use (FOLU) sectors contribute emission based on BAU projected 2030 of 714 Mt CO2e and emission reduction for both unconditional (Counter Measure, CM1) of 17.2% and conditional (CM2) of 24.5%. FOLU emissions correlated with changes in the primary forest to secondary (degradation) and primary/secondary forest to other uses for agriculture, transmigration, plantations and others (deforestation). Due to climate change, the conditions of degradation and deforestation can bring disaster, especially triggered by hydrometeorological hazards that have catastrophic impacts such as floods, flash floods, droughts, erosion, and abrasion due to changes in land cover. Therefore, low carbon development strategies from the forestry sector are needed to reduce climate-related disasters in West Papua.
Assessment of the Coastal Vulnerability Index (CVI) for disaster mitigation strategies in some coastal tourism areas in Gunungkidul, Yogyakarta-Indonesia
Authors: Widura Elsa , Mardiatno Djati
Published: February 2022

South coastal area of Gunungkidul, Yogyakarta-Indonesia has a high tourism development due to the unique physical conditions of coastal typology. However, during the last few years, extreme wave height associated with cyclones damaged many tourist facilities there. Coastal management for ecosystem sustainability requires disaster mitigation, which one considering the aspect of vulnerability. This study aims to assess the level of coastal vulnerability according to coastal typology of Baron-Pok Tunggal section and to determine the coastal management model based on the level of vulnerability. The Coastal Vulnerability Index (CVI) is used in vulnerability assessment. The variable formulation of CVI is divided into hydrodynamic factors (mean significant wave heights, mean tide range, and mean sea level rise) and morphodynamics factors, i.e. geomorphology, coastal slope, and average width of emerged beach. The morphodynamics data were obtained through observation, direct measurements in the field by systematic sampling, extraction from aerial photographs and digital surface model (DSM). The results of modeling and predictions by several agencies are derived to obtain the hydrodynamics data. The result of this study revealed that marine deposition coast typology have a high and moderate vulnerability (twelve and eleven coastal units, respectively). Meanwhile, a low vulnerability can be found in the cliff coast or wave erosion coast typology (24 units). The convex or concave beaches tend to be more vulnerable than beaches with the straight form. The beaches of Buluk, Drini, Kosakora, Sarangan and all beaches from Krakal to Indrayanti have a high vulnerability. Geomorphological variables, significant wave height, and sea level rise have the strongest influence on vulnerability. Coastal management in the marine deposition coast typology can be carried out either in a protective manner or by accommodative approach, such as by observing changes in natural conditions due to sea level rise.
The analysis of coastline changes of maruni beach in Manokwari during 1995-2021 period
Authors: Tapilatu Maryrose E. , Siburian Rima H. S. , Tapilatu Ricardo F.
Published: February 2022

The coastal area of Maruni at Manokwari Regency is known for its potential as a fish-producing area, industry, settlements, ports, and others. However, some parts of Maruni coastal areas have been damaged due to the development. The coastal area experienced changes caused by both natural processes and human activities. The presence of natural and artificial processes in coastal areas results in accretion and abrasion. The dynamics of oceanographic pressures such as sea tidal, sea waves, ocean currents, and tides occurring in the Maruni Beach area cause changes in the movement of sediments affecting the coastal area. Continuous changes can be a threat to Maruni coastal line as the Trans Papua Barat Road passed this route. This research was conducted with the aim to quantify the rate of coastline changes and oceanographic dynamics of Maruni coastal line at the south part of Manokwari Regency, Papua Barat Province from 1995 to 2021. The utilization of remote sensing interpretation method from Landsat 5 TM, Landsat 8 OLI, and oceanographic data providers (BIG, ECMWF) accommodated data source. The analysis result concluded that changes in the coastline at Maruni Coastal line during the 1995-2021 period predominantly encountered abrasion. The magnitude rate of change experienced a very small accretion, but was replaced by a very high abrasion event that occurred during two observation periods between 1995-2021.
Protection of the elderly in disaster situations in Indonesia
Authors: Tukino
Published: February 2022

The territory of Indonesia is an area that is prone to disasters, both natural, non-natural and social disasters. Thus, the elderly in Indonesia live in a situation of threat of disaster. This study uses a secondary data research method with locus is focused on areas of Indonesia where disasters have occurred in the last five years from 2016 to 2020, namely; earthquake in Pidie Jaya, earthquake and tsunami in Lombok, earthquake and tsunami in Palu, social disaster in Mempawah-West Kalimantan, flash floods in Garut, and the Covid-19 disaster. The data collected was then analyzed using document analysis techniques.

Our analysis result concluded that the absence of caregiver who specifically provide programmed assistance, makes the elderly feel lonely, stressed and traumatized. Social workers contribute to the handling of the elderly in disaster locations focused on psychosocial support, and advocacy of legislative policies.
Identification of Land Use and Land Change due to its impact on Groundwater Level in Surakarta city
Authors: Koesuma Sorja , Sunaryo  , Handono Ramelan Ari , Sutarno Doddy
Published: February 2022

Surakarta City is the center of economic activity in the great Solo area. As a result, land use changes occur very quickly. This study aims to identify land use and land changes due to their effects on groundwater levels in Surakarta City. The method used in this research is a descriptive-quantitative method. The analysis technique used is time series, by comparing image data for 2003, 2008, and 2019. The image is obtained from Google Earth and then visually interpreted in a GIS application to get the land use area. Land use in Surakarta City includes buildings, agriculture, vacant land, tourist land, waters, settlements, green open spaces, rice fields, shrubs, and dryland agriculture. The results of image processing show that there is a change in land use in Surakarta City. The results show that there is a relationship between land use/change with an increase in population and ground water use. The areas most affected by the decline in groundwater are in the central part of the city of Surakarta, especially in the villages of Sangkrah and Semanggi.
Proposed scenario of low carbon development from waste sector in West Papua
Authors: Raharjo Syafrudin , Prabawardani Saraswati , Hendri  , Suarga Egi , Faruk Rosyaridho M , Ida Suriany , Kalmirah Julia
Published: February 2022

The increasing of population and economic growth, urbanization, development progress and living standard has accelerated the rate and amount of waste generation. Waste is a serious problem of a worldwide concern because of its impact on environmental pollution, health and flood disasters in some drainages and rivers. Proper waste management is needed to reduce or prevent its negative impacts. For this reason, it is necessary to identify the types of waste and their potential to produce greenhouse gas emissions in order to obtain an accurate picture in an effort to formulate policies and strategies for reducing GHG emissions. The method used was thinking system and dynamic system by looking at the BAU scenario, 29%, 41% and 44% emission reduction. Based on the model of the dynamics system, a new scenario is needed through the intervention of waste processing by 3R at TPS and TPA, applying aerobic composting, methane capture and incineration.
Coral Reef Damage Caused by The Indinurmatalia07 Grounding in Cross-over Reef, Lemon Island of Manokwari Papua Barat Province
Authors: Sitanala Alex R. , Krey Hance , Rumfabe Marthen , Rumbekwan Nelman , Sanyar Melkias , Hein Biloro Rimer , Mofu Muda , Krey Vecky , Alzair Nur , Tapilatu Ricardo F.
Published: February 2022

The cargo ship, Indi Nurmatalia07, ran aground on 07 August, 2021 at 23.00 at ‘Cross Over’ reef in the Dorery Bay – Manokwari. The interim report revealed that the ship’s officer was not able to control the ship when it left Manokwari port due to bad weather condition when the ship left at 19.00. However, report on the cause of bad weather was doubtful because the distance between the port of Manokwari and the incident site is only about 500m. The vessel was later freed from the reef on 10 August 2021 at 19.00 after disembarking shipload. An initial quantitative assessment of damages was conducted by a local team within the grounding site. Four line transect surveys were conducted, each 25m in length and 2m in width, positioned in the left and right of the damaged and undamaged area. Our initial results demonstrated that a total area of 717,02m2has been damaged by the cargo ship. The type of coral reef formation is patch reef with medium diversity of coral species (mainly genusAcropora,Pocillopora,Coeloseris,Millepora, andGoniopora) and coral cover. Cross over reef has a shallow reef top (between 3-10m depth), slopes down to at least 25m. The reef is subject to high velocity current that might be unsuitable for coral planula to settle permanently. Coral structures were partly crushed and fractured at the edge of the damaged area but totally damaged in central part. The central damaged site has lost remarkable bottom coral structure and diversity from at least 5 different coral genera. By using a comparison study conducted on ship groundings, the Provincial government would sue the cargo ship and insurance company to pay environmental losses due to environmental based on a calculation which considered damage in relation to the ecosystem, economy, society and ecosystem rehabilitation referring to PerMen LH No. 7/2014.
Subnanosecond widely-tunable in the visible spectrum range LBO based optical parametric amplifier
Authors: Stanionytė G , Vėjalytė E , Tamulienė V , Jarutis V , Vengelis J
Published: February 2022

We report realization of a widely-tunable subnanosecond optical parametric amplifier system in LBO crystal pumped by third harmonic of a passively Q-switched Nd:YAG microlaser system. It yields continuous signal wavelength tunability in the visible spectrum range from 460 to 680 nm and idler wavelength — from 740 to 1500 nm. We present experimental data and numerical simulations of our optical parametric amplifier and discuss future improvement directions for greater pump to signal conversion efficiency.
Prompt acceleration of a μ
+ beam in a toroidal wakefield driven by a shaped steep-rising-front Laguerre–Gaussian laser pulse
Authors: Wang Xiaonan , LAN Xiaofei , HUANG Yongsheng , JIANG Youge , ZHANG Chunlei , ZHANG Hao , YU Tongpu
Published: February 2022

Recent experimental data for anomalous magnetic moments strongly indicates the existence of new physics beyond the Standard Model. Energetic μ
+ bunches are relevant to μ
+ rare decay, spin rotation, resonance and relaxation (μSR) technology, future muon colliders, and neutrino factories. In this paper, we propose prompt μ
+ acceleration in a nonlinear toroidal wakefield driven by a shaped steep-rising-front Laguerre–Gaussian (LG) laser pulse. An analytical model is described, which shows that a μ
+ beam can be focused by an electron cylinder at the centerline of a toroidal bubble and accelerated by the front part of the longitudinal wakefield. A shaped LG laser with a short rise time can push plasma electrons, generating a higher-density electron sheath at the front of the bubble, which can enhance the acceleration field. The acceleration field driven by the shaped steep-rising-front LG laser pulse is about four times greater than that driven by a normal LG laser pulse. Our simulation results show that a 300 MeV μ
+ bunch can be accelerated to 2 GeV and its transverse size is focused from an initial value of w
0 = 5 μm to w = 2 μm in the toroidal bubble driven by the shaped steep-rising-front LG laser pulse with a normalized amplitude of a = 22.
Acute elevation of liver function test values following concomitant administration of dabigatran and primidone
Authors: Caviness Lisa A , Wassell Katelyn M , Howard-Thompson Amanda
Published: February 2022

Purpose

We report a unique case of transiently elevated liver function test (LFT) values associated with concurrent use of dabigatran and primidone, which has not previously been described in the scientific literature.

Management of drug-drug interactions requires a fundamental understanding of pharmacodynamic and pharmacokinetic parameters. Despite the use of available best predictive models, idiosyncratic drug reactions may still occur when a newly approved medication begins to be used in the general population. We report a case of a possible interaction (Naranjo adverse drug reaction probability score of 3, Roussel Uclaf causality assessment method score of 3) between dabigatran and primidone in a 70-year-old Caucasian male resulting in a transient elevation of LFT values. The patient was transitioned from warfarin to dabigatran in the setting of persistently subtherapeutic international normalized ratio values. During a routine outpatient follow-up appointment approximately 1 month after dabigatran initiation, the patient was discovered to have LFT values greater than 5 times the upper limit of normal. Dabigatran was thus discontinued; the patient was returned to warfarin therapy and their LFT values returned to baseline.

Conclusion

Studies have indicated a potential for reduced dabigatran efficacy with concurrent use of primidone due to P-glycoprotein induction, thereby potentiating the risk for thrombosis. To date, reports of this interaction resulting in hepatic injury are lacking. The present case suggests that this interaction may be clinically significant with regard to selection of antithrombotic medication therapy in patients on primidone therapy.
Evaluation of machine learning models on protein level inference from prioritized RNA features
Authors: Xu Wenjian , He Haochen , Guo Zhengguang , Li Wei
Published: February 2022

The parallel measurement of transcriptome and proteome revealed unmatched profiles. Since proteomic analysis is more expensive and challenging than transcriptomic analysis, the question of how to use messenger RNA (mRNA) expression data to predict protein level is extremely important. Here, we comprehensively evaluated 13 machine learning models on inferring protein expression levels using RNA expression profile. A total of 20 proteogenomic datasets from three mainstream proteomic platforms with >2500 samples of 13 human tissues were collected for model evaluation. Our results highlighted that the appropriate feature selection methods combined with classical machine learning models could achieve excellent predictive performance. The voting ensemble model outperformed other candidate models across datasets. Adding the mRNA proxy model to the regression model further improved the prediction performance. The dataset and gene characteristics could affect the prediction performance. Finally, we applied the model to the brain transcriptome of cerebral cortex regions to infer the protein profile for better understanding the functional characteristics of the brain regions. This benchmarking work not only provides useful hints on the inherent correlation between transcriptome and proteome, but also has practical value of the transcriptome-based prediction of protein expression levels.
A statistical framework for recovering pseudo-dynamic networks from static data
Authors: Chen Chixiang , Shen Biyi , Ma Tianzhou , Wang Ming , Wu Rongling
Published: February 2022

Motivation

The collection of temporal or perturbed data is often a prerequisite for reconstructing dynamic networks in most cases. However, these types of data are seldom available for genomic studies in medicine, thus significantly limiting the use of dynamic networks to characterize the biological principles underlying human health and diseases.

Results

We proposed a statistical framework to recover disease risk-associated pseudo-dynamic networks (DRDNet) from steady-state data. We incorporated a varying coefficient model with multiple ordinary differential equations to learn a series of networks. We analyzed the publicly available Genotype-Tissue Expression data to construct networks associated with hypertension risk, and biological findings showed that key genes constituting these networks had pivotal and biologically relevant roles associated with the vascular system. We also provided the selection consistency of the proposed learning procedure and evaluated its utility through extensive simulations.

Availability and implementation

DRDNet is implemented in the R language, and the source codes are available at https://github.com/chencxxy28/DRDnet/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Short-term safety outcomes of mastectomy and immediate prepectoral implant-based breast reconstruction: Pre-BRA prospective multicentre cohort study
Authors: Harvey Kate L , Sinai Parisa , Mills Nicola , White Paul , Holcombe Christopher , Potter Shelley ,   Pre-BRA Feasibility Study Steering Group, Barry Peter , O'Connell Rachel , Cawthorn Simon , Gardiner Matthew , Irwin Gareth , Kirwan Cliona , McKenzie Mairead , McKenzie Shireen , Oni Georgette , Whisker Lisa , Rattay Tim , Roy Pankaj , Skillman Joanna , Soumian Soni , Vidya Raghavan , Williams Samantha
Published: February 2022

Background

Prepectoral breast reconstruction (PPBR) has recently been introduced to reduce postoperative pain and improve cosmetic outcomes in women having implant-based procedures. High-quality evidence to support the practice of PPBR, however, is lacking. Pre-BRA is an IDEAL stage 2a/2b study that aimed to establish the safety, effectiveness, and stability of PPBR before definitive evaluation in an RCT. The short-term safety endpoints at 3 months after surgery are reported here.

Methods

Consecutive patients electing to undergo immediate PPBR at participating UK centres between July 2019 and December 2020 were invited to participate. Demographic, operative, oncology, and complication data were collected. The primary outcome was implant loss at 3 months. Other outcomes of interest included readmission, reoperation, and infection.

Results

Some 347 women underwent 424 immediate implant-based reconstructions at 40 centres. Most were single-stage direct-to-implant (357, 84.2 per cent) biological mesh-assisted (341, 80.4 per cent) procedures. Conversion to subpectoral reconstruction was necessary in four patients (0.9 per cent) owing to poor skin-flap quality. Of the 343 women who underwent PPBR, 144 (42.0 per cent) experienced at least one postoperative complication. Implant loss occurred in 28 women (8.2 per cent), 67 (19.5 per cent) experienced an infection, 60 (17.5 per cent) were readmitted for a complication, and 55 (16.0 per cent) required reoperation within 3 months of reconstruction.

Conclusion

Complication rates following PPBR are high and implant loss is comparable to that associated with subpectoral mesh-assisted implant-based techniques. These findings support the need for a well-designed RCT comparing prepectoral and subpectoral reconstruction to establish best practice for implant-based breast reconstruction.
Functional mapping and cooperation between the cerebellum and cerebrum during word reading
Authors: Li Hehui , Wu Junjie , Marks Rebecca A , Huang Huiya , Li Lina , Dong Lin , Luo Yue-Jia , Tao Wuhai , Ding Guosheng
Published: February 2022

Multiple areas in the cerebellum have been reported to be engaged in reading. However, how these regions cooperate with the reading-related areas in the cerebrum remains unclear. Here, brain images of fifty-two adults were acquired via functional magnetic resonance imaging. By comparing the cerebellar activation across three localization tasks targeting orthographic, phonological, and semantic processing, we first identified three different reading-related areas in the cerebellum, biased toward orthography, phonology, and semantics, respectively. Then, functional connectivity (FC) analyses demonstrated that the mean FC between functionally corresponding areas across the cerebrum and cerebellum was greater than that between noncorresponding areas during silent word reading. FC patterns of functionally corresponding areas could significantly predict reading speed, with the FC driven from orthographic and semantic areas contributing the most. Effective FC analyses further showed that orthographic and semantic areas in the cerebellum had selective and direct connectivity to areas in the cerebrum with similar functional specificity. These results suggest that reading-related areas vary in their functions to reading, and cooperation between areas with corresponding functions was greater than that between noncorresponding areas. These findings emphasize the importance of functional cooperation between the cerebrum and cerebellum during reading from a new perspective.
ImmuneData: an integrated data discovery system for immunology data repositories
Authors: Deng Nan , Wu Canglin , Yaseen Ashraf , Wu Hulin
Published: February 2022

To meet the increasing demand for data sharing, data reuse and meta-analysis in the immunology research community, we have developed the data discovery system ImmuneData. The system provides integrated access to five immunology data repositories funded by the National Institute of Allergy and Infectious Diseases, Division of Allergy, Immunology and Transplantation, including ImmPort, ImmuneSpace, ITN TrialShare, ImmGen and IEDB. ImmuneData restructures the data repositories’ metadata into a uniform schema using domain experts’ knowledge and state-of-the-art Natural Language Processing (NLP) technologies. It comes with a user-friendly web interface, accessible at http://www.immunedata.org/, and a Google-like search engine for biological researchers to find and access data easily. The vast quantity of synonyms used in biomedical research increase the likelihood of incomplete search results. Thus, our search engine converts queries submitted by users into ontology terms, which are then expended by NLP technologies to ensure that the search results will include all synonyms for a particular concept. The system also includes an advanced search function to build customized queries to meet higher-level users’ needs. ImmuneData ensures the FAIR principle (Findability, Accessibility, Interoperability and Reusability) of the five data repositories to benefit data reuse in the immunology research community. The data pipeline constructing our system can be extended to other data repositories to build a more comprehensive biological data discovery system.

Database URL

http://www.immunedata.org/
Correlation between respiratory muscle weakness and frailty status as risk markers for poor outcomes in patients with cardiovascular disease
Authors: Hamazaki Nobuaki , Kamiya Kentaro , Nozaki Kohei , Yamashita Masashi , Uchida Shota , Noda Takumi , Maekawa Emi , Meguro Kentaro , Yamaoka-Tojo Minako , Matsunaga Atsuhiko , Ako Junya
Published: February 2022

Aims

Although the developmental mechanism of respiratory muscle weakness (RMW) and frailty are partly similar in patients with cardiovascular disease (CVD), their relationship remains unclear. This study aimed to investigate the correlation between RMW and frailty and its impact on clinical outcomes in patients with CVD.

Methods and results

In this retrospective observational study, consecutive 1217 patients who were hospitalized for CVD treatment were enrolled. We assessed frailty status by using the Fried criteria and respiratory muscle strength by measuring the maximal inspiratory pressure (PImax) at hospital discharge, with RMW defined as PImax <70% of the predicted value. The endpoint was a composite of all-cause death and/or readmission for heart failure. We examined the prevalence of RMW and frailty and their correlation. The relationships of RMW with the endpoint for each presence or absence of frailty were also investigated. Respiratory muscle weakness and frailty were observed in 456 (37.5%) and 295 (24.2%) patients, respectively, and 149 (12.2%) patients had both statuses. Frailty was detected as a significant indicator of RMW [odds ratio: 1.84, 95% confidence interval (CI): 1.39–2.44]. Composite events occurred in 282 patients (23.2%). Respiratory muscle weakness was independently associated with an increased incidence of events in patients with both non-frailty [hazard ratio (HR): 1.40, 95% CI: 1.04–1.88] and frailty (HR: 1.68, 95% CI: 1.07–2.63).

Conclusions

This is the first to demonstrate a correlation between RMW and frailty in patients with CVD, with 12.2% of patients showing overlap. RMW was significantly associated with an increased risk of poor outcomes in patients with CVD and frailty.
Tricuspid regurgitation after cardiac resynchronization therapy: evolution and prognostic significance
Authors: Stassen Jan , Galloo Xavier , Hirasawa Kensuke , Marsan Nina Ajmone , van der Bijl Pieter , Delgado Victoria , Bax Jeroen J
Published: February 2022

Aims

Tricuspid regurgitation (TR) is common in patients with heart failure (HF) and is associated with worse outcome. This study investigated the effect of cardiac resynchronization therapy (CRT) on TR severity and long-term outcome.

Methods and results

Tricuspid regurgitation severity was assessed at baseline and 6 months after CRT implantation, using a multiparametric approach. Patients were divided into four groups: (i) no or mild TR without progression; (ii) no or mild TR with progression to significant (moderate–severe) TR; (iii) significant TR with improvement to no or mild TR; and (iv) significant TR without improvement. The primary endpoint was all-cause mortality. A total of 852 patients (mean age 65 ± 11 years, 77% male) were included. At baseline, 184 (22%) patients had significant TR, with 75 (41%) showing significant improvement at 6-month follow-up. After a median follow-up of 92 (50–137) months, 494 (58%) patients died. Patients with significant TR showing improvement at follow-up had better outcomes than those showing no improvement (P = 0.016). On multivariable analysis, no or mild TR progressing to significant TR [hazard ratio (HR) 1.745; 95% confidence interval (CI): 1.287–2.366; P < 0.001] and significant TR without improvement (HR 1.572; 95% CI: 1.198–2.063; P = 0.001) were independently associated with all-cause mortality, whereas significant TR with improvement at follow-up was not (HR: 1.153; 95% CI: 0.814–1.633; P = 0.424).

Conclusion

Improvement of significant TR after CRT is observed in a substantial proportion of patients, highlighting the potential benefit of CRT for patients with HF having significant TR. Significant TR at 6 months after CRT is independently associated with increased long-term mortality.
Opportunities and limitations of thinning to increase resistance and resilience of trees and forests to global change
Authors: Moreau Guillaume , Chagnon Catherine , Achim Alexis , Caspersen John , D’Orangeville Loïc , Sánchez-Pinillos Martina , Thiffault Nelson
Published: February 2022

We reviewed recent literature to identify the positive and negative effects of thinning on both stand- and tree-level resistance and resilience to four stressors that are expected to increase in frequency and/or severity due to global change: (1) drought, (2) fire, (3) insects and pathogens, and (4) wind. There is strong evidence that thinning, particularly heavy thinning, reduces the impact of drought and also the risk and severity of fire when harvest slash is burned or removed. Thinning also increases the growth and vigor of residual trees, making them less susceptible to eruptive insects and pathogens, while targeted removal of host species, susceptible individuals and infected trees can slow the spread of outbreaks. However, the evidence that thinning has consistent positive effects is limited to a few insects and pathogens, and negative effects on root rot infection severity were also reported. At this point, our review reveals insufficient evidence from rigorous experiments to draw general conclusions. Although thinning initially increases the risk of windthrow, there is good evidence that thinning young stands reduces the long-term risk by promoting the development of structural roots and favouring the acclimation of trees to high wind loads. While our review suggests that thinning should not be promoted as a tool that will universally increase the resistance and resilience of forests, current evidence suggests that thinning could still be an effective tool to reduce forest vulnerability to several stressors, creating a window of opportunity to implement longer term adaptive management strategies such as assisted migration. We highlight knowledge gaps that should be targeted by future research to assess the potential contribution of thinning to adaptive forest management. One of these gaps is that studies from boreal and tropical regions are drastically underrepresented, with almost no studies conducted in Asia and the southern hemisphere. Empirical evidence from these regions is urgently needed to allow broader-scale conclusions.
An In Vivo Stable Isotope Labeling Method to Investigate Individual Matrix Protein Synthesis, Ribosomal Biogenesis, and Cellular Proliferation in Murine Articular Cartilage
Authors: Kobak Kamil A , Batushansky Albert , Borowik Agnieszka K , Lopes Erika Prado Barboza , Peelor III Frederick F , Donovan Elise L , Kinter Michael T , Miller Benjamin F , Griffin Timothy M
Published: February 2022

Targeting chondrocyte dynamics is a strategy for slowing osteoarthritis progression during aging. We describe a stable-isotope method using in vivo deuterium oxide labeling and mass spectrometry to measure protein concentration, protein half-life, cell proliferation, and ribosomal biogenesis in a single sample of murine articular cartilage. We hypothesized that a 60-d labeling period would capture age-related declines in cartilage matrix protein content, protein synthesis rates, and cellular proliferation. Knee cartilage was harvested to the subchondral bone from 25- to 90-wk-old female C57BL/6J mice treated with deuterium oxide for 15, 30, 45, and 60 d. We measured protein concentration and half-lives using targeted high resolution accurate mass spectrometry and d2ome data processing software. Deuterium enrichment was quantified in isolated DNA and RNA to measure cell proliferation and ribosomal biogenesis, respectively. Most collagen isoforms were less abundant in aged animals, with negligible collagen synthesis at either age. In contrast, age altered the concentration and half-lives of many proteoglycans and other matrix proteins, including several with greater concentration and half-lives in older mice such as proteoglycan 4, clusterin, and fibronectin-1. Cellular proteins were less abundant in older animals, consistent with reduced cellularity. Nevertheless, deuterium was maximally incorporated into 60% of DNA and RNA by 15 d of labeling in both age groups, suggesting the presence of two large pools of either rapidly (<15 d) or slowly (>60 d) proliferating cells. Our findings indicate that age-associated changes in cartilage matrix protein content and synthesis occur without detectable changes in the relative number of proliferating cells.
Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere
Authors: Spang Anja , Mahendrarajah Tara A , Offre Pierre , Stairs Courtney W
Published: February 2022

The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.
Extend mixed models to multilayer neural networks for genomic prediction including intermediate omics data
Authors: Zhao Tianjing , Zeng Jian , Cheng Hao
Published: February 2022

With the growing amount and diversity of intermediate omics data complementary to genomics (e.g. DNA methylation, gene expression, and protein abundance), there is a need to develop methods to incorporate intermediate omics data into conventional genomic evaluation. The omics data help decode the multiple layers of regulation from genotypes to phenotypes, thus forms a connected multilayer network naturally. We developed a new method named NN-MM to model the multiple layers of regulation from genotypes to intermediate omics features, then to phenotypes, by extending conventional linear mixed models (“MM”) to multilayer artificial neural networks (“NN”). NN-MM incorporates intermediate omics features by adding middle layers between genotypes and phenotypes. Linear mixed models (e.g. pedigree-based BLUP, GBLUP, Bayesian Alphabet, single-step GBLUP, or single-step Bayesian Alphabet) can be used to sample marker effects or genetic values on intermediate omics features, and activation functions in neural networks are used to capture the nonlinear relationships between intermediate omics features and phenotypes. NN-MM had significantly better prediction performance than the recently proposed single-step approach for genomic prediction with intermediate omics data. Compared to the single-step approach, NN-MM can handle various patterns of missing omics measures and allows nonlinear relationships between intermediate omics features and phenotypes. NN-MM has been implemented in an open-source package called “JWAS”.
Crustal and uppermost mantle structure of the NW Namibia continental margin and the Walvis Ridge derived from ambient seismic noise
Authors: Ryberg T , Geissler W H , Jokat W , Yuan X , Fromm T , Pandey S , Heit B
Published: February 2022

The Walvis Ridge (WR) is the most prominent hotspot track related to the opening in the South Atlantic Ocean. Several hypotheses have been developed to explain its origin and evolution. The presence of a massive magmatic structure at the landfall of the WR in Northwest Namibia raised speculation about the role of a hotspot during the opening of the South Atlantic ocean. To investigate its deeper velocity structure at the junction of the WR with the African continent was the focus of the amphibious seismological WALPASS experiment. In total 12 ocean-bottom seismometers and 28 broad-band land stations were installed between 2010 and 2012 to acquire seismological data. Here, we present the results of seismic ambient noise tomography to investigate to which extent the Tristan hotspot modified the crustal structure in the landward prolongation of the ridge and in the adjacent oceanic basins. For the tomography, vertical and hydrophone component cross correlations for >300 d for OBS stations and between 1 and 2 yr for land stations data were analysed. More than 49 000 velocity measurements (742 dispersion curves) were inverted for group velocity maps at 75 individual signal periods, which then had been inverted for a regional 3-D shear wave velocity model. The resulting 3-D model reveals structural features of the crust related to the continent–ocean transition and its disturbance caused by the initial formation of the WR ∼130 Ma. We found relatively thick continental crust below Northwest Namibia and below the near-shore part of the WR, a strong asymmetry offshore with typical, thin oceanic crust in the Namibe Basin (crossing over into the Angola Basin further offshore) to the North and a wide zone of transitional crust towards the Walvis Basin south of the WR.
The crustal configuration of the West and Central African Rift System from gravity and seismic data analysis
Authors: Ghomsi Franck Eitel Kemgang , Tenzer Robert , Njinju Emmanuel , Steffen Rebekka
Published: February 2022

The West and Central African Rift System (WCARS) is the only stable continental geological structure on Earth that is formed by large-scale topographic massifs (swells). However, knowledge of the origin and evolution of the WCARS remains limited mainly due to the scarcity of high-resolution geophysical observations. To better understand the crustal structure beneath the entire WCARS, we use the XGM2016 global gravitational model and the ETOPO1 global topographic-bathymetric model to determine a gravimetric Moho (crust-mantle boundary) model constrained by seismic Moho depth estimates at 41 seismological stations distributed irregularly within the study area. The result reveals a regional Moho deepening to ∼40 km beneath the Hoggar, Aïr and Tibesti Massifs. The largest Moho deepening to ∼46 km is detected beneath the Archean Congo Craton, while the Moho depth under the Adamawa Plateau reaches 42 km. The Moho geometry beneath the Chad Basin, the Chad Lineament and the Termit Basin is relatively even with the Moho depth mostly within 24–26 km. A significant Moho deepening as well as large Moho depth variations within 32–45 km beneath the Saharan Metacraton and the Congo Craton (especially under its northern margin) reflect the metacratonization processes that occurred during the Neoproterozoic. The Niger Delta and the Benue Trough are characterized by a very thin continental crust with the Moho depth varying from ∼20 km in the south along the Atlantic coastline to ∼24 km in the northeastern branch of the Cretaceous Benue Trough around the Garoua-Yola Rift.
Peterman's productivity method for estimating dynamic reference points in changing ecosystems
Authors: Silvar-Viladomiu Paula , Minto Cóilín , Brophy Deirdre , Reid David G
Published: February 2022

Target and limit reference points are fundamental management components used to define sustainable harvest strategies. Maximum Sustainable Yield (MSY) and the precautionary principle underpin many reference points. Non-proxy reference points based on MSY in age-based single-species assessments depend on the stock–recruitment (SR) relationship, which can display complex variability. Current reference points ignore persistent dynamic change by assuming that the SR relationship is stationary and with constant recruitment parameters over selected time periods. We highlight Peterman's productivity method (PPM), which is capable of tracking temporal dynamics of recruitment productivity via time-varying SR parameters. We show how temporal variability in SR parameters affects fishing mortality and biomass MSY-based reference points. Implementation of PPM allows for integrated dynamic ecosystem influences in tactical management while avoiding overwrought and sometimes ephemeral mechanistic hypotheses tested on small and variable SR datasets. While some of these arguments have been made in individual papers, in our opinion the method has not yet garnered the attention that is due to it.
The Stuff from the Siege: Transitional Justice and the Power of Everyday Objects in Museums
Authors: Mannergren Selimovic Johanna
Published: February 2022

ABSTRACT∞

This article explores the role of the affective power of everyday objects in commemorations of war and conflict. It seeks to understand the transformative power of the everyday as a memory node and investigates how and why everyday objects can become carriers of an inclusive rendering of the past. Through a phenomenologically grounded reading of two exhibitions on the 1992–1995 siege of the Bosnian capital Sarajevo, the article theoretically advances the idea that everyday objects that are transformed into artefacts in museums expand our moral, mnemonic imagination and therefore potentially contribute to peace. A systematic analysis of the affective power of everyday objects is developed through three key conceptual lenses – authenticity, intimacy and vulnerability. The study thus contributes to research on the postwar museum as a site for transitional justice and peacebuilding, and the role of material things as carriers of emotions and meaning in the context of postwar memorialization.
Ancient and recent differences in the intrinsic susceptibility of Mycobacterium tuberculosis complex to pretomanid
Authors: Bateson Anna , Ortiz Canseco Julio , McHugh Timothy D. , Witney Adam A. , Feuerriegel Silke , Merker Matthias , Kohl Thomas A. , Utpatel Christian , Niemann Stefan , Andres Sönke , Kranzer Katharina , Maurer Florian P , Ghodousi Arash , Borroni Emanuele , Cirillo Daniela Maria , Wijkander Maria , Toro Juan C. , Groenheit Ramona , Werngren Jim , Machado Diana , Viveiros Miguel , Warren Robin M. , Sirgel Frederick , Dippenaar Anzaan , Köser Claudio U. , Sun Eugene , Timm Juliano
Published: February 2022

Objectives

To develop a robust phenotypic antimicrobial susceptibility testing (AST) method with a correctly set breakpoint for pretomanid (Pa), the most recently approved anti-tuberculosis drug.

Methods

The Becton Dickinson Mycobacterial Growth Indicator Tube™ (MGIT) system was used at six laboratories to determine the MICs of a phylogenetically diverse collection of 356 Mycobacterium tuberculosis complex (MTBC) strains to establish the epidemiological cut-off value for pretomanid. MICs were correlated with WGS data to study the genetic basis of differences in the susceptibility to pretomanid.

Results

We observed ancient differences in the susceptibility to pretomanid among various members of MTBC. Most notably, lineage 1 of M. tuberculosis, which is estimated to account for 28% of tuberculosis cases globally, was less susceptible than lineages 2, 3, 4 and 7 of M. tuberculosis, resulting in a 99th percentile of 2 mg/L for lineage 1 compared with 0.5 mg/L for the remaining M. tuberculosis lineages. Moreover, we observed that higher MICs (≥8 mg/L), which probably confer resistance, had recently evolved independently in six different M. tuberculosis strains. Unlike the aforementioned ancient differences in susceptibility, these recent differences were likely caused by mutations in the known pretomanid resistance genes.

Conclusions

In light of these findings, the provisional critical concentration of 1 mg/L for MGIT set by EMA must be re-evaluated. More broadly, these findings underline the importance of considering the global diversity of MTBC during clinical development of drugs and when defining breakpoints for AST.
Early phenotypic detection of fluconazole- and anidulafungin-resistant Candida glabrata isolates
Authors: Georgiou Panagiota-Christina , Arendrup Maiken Cavling , Meletiadis Joseph
Published: February 2022

Background

Increased fluconazole and echinocandin resistance in Candida glabrata requires prompt detection in routine settings. A phenotypic test based on the EUCAST E.DEF 7.3.2 protocol was developed for the detection of fluconazole- and anidulafungin-resistant isolates utilizing the colorimetric dye XTT.

Methods

Thirty-one clinical C. glabrata isolates, 11 anidulafungin resistant and 14 fluconazole resistant, were tested. After optimization studies, 0.5–2.5 × 105 cfu/mL of each isolate in RPMI 1640 + 2% d-glucose medium containing 100 mg/L XTT + 0.78 μΜ menadione and 0.06 mg/L anidulafungin (S breakpoint) or 16 mg/L fluconazole (I breakpoint) in 96-well flat-bottom microtitration plates were incubated at 37°C for 18 h; we also included drug-free wells. XTT absorbance was measured at 450 nm every 15 min. Differences between the drug-free and the drug-treated wells were assessed using Student’s t-test at different timepoints. ROC curves were used in order to identify the best timepoint and cut-off.

Results

The XTT absorbance differences between fluconazole-containing and drug-free wells were significantly lower for the resistant isolates compared with susceptible increased exposure isolates (0.08 ± 0.05 versus 0.25 ± 0.06, respectively, P = 0.005) at 7.5 h, with a difference of <0.157 corresponding to 100% sensitivity and 94% specificity for detection of resistance. The XTT absorbance differences between anidulafungin-containing and drug-free wells were significantly lower for the resistant isolates compared with susceptible isolates (0.08 ± 0.07 versus 0.200 ± 0.03, respectively, P < 0.001) at 5 h, with a difference of <0.145 corresponding to 91% sensitivity and 100% specificity, irrespective of underlying mutations.

Conclusions

A simple, cheap and fast phenotypic test was developed for detection of fluconazole- and anidulafungin-resistant C. glabrata isolates.
Accuracy of preoperative staging of gastric stump cancer
Authors: Kiyokawa Takashi , Fukagawa Takeo , Kaneshiro Shinya , Igarashi Yuuichi , Soeda Naruyoshi , Kumata Yoshimasa , Horikawa Masahiro , Sasajima Yuko , Matsuda Keiji , Fukushima Ryoji
Published: February 2022

Background

In this study, the accuracy of preoperative staging for gastric stump cancer, which has not been thoroughly investigated since the condition is rare, was investigated using computed tomography and gastroscopic imaging.

Methods

Between February 1994 and April 2018, 49 patients with gastric stump cancer, following subtotal or total gastrectomy, were reviewed retrospectively. Preoperative diagnoses of clinical T and clinical N categories were compared with post-operative pathological diagnoses (pT and pN categories). Positive predictive values, accuracy, sensitivity and specificity were also evaluated.

Results

The overall accuracy of T staging was 40.8%. The positive predictive value for cT3/T4 was 96.3%, whereas the positive predictive value for cT1/T2 was 72.7%. The overall accuracy for N staging was 61.2%. The positive predictive value of lymph node positive patients was 73.3%. The positive predictive value and sensitivity of over stage II were 96.6% and 84.8%, respectively.

Conclusions

The accuracy of preoperative diagnosis using both computed tomography and gastroscopy imaging may be feasible for T3/T4 advanced gastric stump cancer, whereas diagnosing T1/2 gastric stump cancer must be carefully considered due to high misdiagnosis rates, relating to depth.
Report of two rare manifestations of abdominal tuberculosis mimicking neoplasia
Authors: Faulhaber Senta , Schindera Sebastian , Hartel Mark , Gräfitsch Alexander
Published: February 2022

Abdominal tuberculosis (TB) can affect any organ of the gastrointestinal tract, and as a result of its unspecific symptoms, it may even mimic neoplasia. Rare manifestations are difficult to detect even for the trained eye and require clinical suspicion. We report rare cases of a mechanical ileus due to peritoneal TB in a 41-year-old man and an isolated peripancreatic infection in a 54-year-old woman. While in one patient, suspected malignancy led to diagnostic laparoscopy, it led to a total pancreatectomy with splenectomy in the other case. However, both times histology ruled out malignancy and showed unexpected similarities with TB. The patients responded well to medical treatment, although one patient is struggling with pancreatogenic diabetes.