bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermophysical properties of Cordyceps militaris change during the freezing process
Authors: Nguyen Van – Phuc , Nguyen Nguyen-An , Luong Duc – Vu
Published: December 2023

This study focuses on determining the thermophysical parameters of Cordyceps militaris in the freezing stage of the freeze-drying process. When the temperature of Cordyceps militaris changed from an ambient temperature of 25°C to a freezing temperature of -45°C, the thermophysical parameters of Cordyceps militaris changed much. The study determined the initial freezing point temperature of Cordyceps militaris to be -0.6°C. At temperatures above the initial freezing point, the density (ρ) and specific heat (c) increase slightly as the temperature decreases. In contrast, thermal conductivity (k), thermal diffusivity (a), and enthalpy (h) decrease. However, at temperatures below the initial freezing point, when the temperature decreases, the density, specific heat, and enthalpy decrease while the coefficient of thermal conductivity and thermal diffusion increase. The results obtained from this study can be applied in calculating the heat and mass transfer during the freezing phase in the freeze-drying process of Cordyceps militaris.
Fabrication of activated carbon from Acacia Crassicarpa bark by carbothermal functionalization for adsorptive removal the dyes in aqueous solution
Authors: Nong Mai X T , Nguyen Nam V , Doan Anh T , Nguyen Dat X , Tran Ninh V , Do Tung C , Nguyen Trung D , Nguyen Tue N , Dang Khanh Q
Published: December 2023

Activated carbon adsorbent prepared fromAcacia Crassicarpa barkhas been successfully synthesized via carbonization and chemical activation processes to investigate the elimination of hazardous dyes in industrial wastewater, specifically the anionic dye methyl orange (MO) and the cationic dye methylene blue (MB) in this study. TheAcacia Crassicarpa barkwas washed with distilled water and dried it in an electric oven at 100 °C. The carbonization process was carried out at a temperature of 1050 °C in the Argon atmosphere and thoroughly was activated by NaOH. The results showed that a high BET surface area of 711.05 m2/g was obtained. XRD pattern presented that the high content of crystalline carbon was formed and carbon content was achieved approximately 83%. Also, SEM images illustrated the average size of carbon is 2.58 μm and surface structure of activated carbon appeared the pores inside the particle. The Langmuir was observed to fit the adsorption data well. The maximum equilibrium adsorption capacities predicted by the Langmuir isotherm were found to be 156.25 mg/g and 144.09 mg/g for MO and MB, respectively. All of those results confirm that the activated carbon originated fromAcacia Crassicarpa barkcan potentially be applied for water purification treatment. In comparison to traditional charcoal, this activated carbon presents numerous advantages. Notably, it can integrate into the biomass energy cycle, improve filtration capabilities, and result in cost savings.
Electrical and mechanical response of spin-coated PVDF-TrFE formed from MIBK and DMSO solvents under external excitations
Authors: Riaz Naeem , Wu Nan , Shafai Cyrus
Published: December 2023

Flexible polymer piezoelectric materials are of interest in electro-mechanical applications; however, the mechanical and electrical properties of these materials can be affected by their formation. In this study vibrational analysis was performed to explore the mechanical and electrical properties of piezoelectric PVDF-TrFE polymer using external excitations. Frequency response study of cantilever cantilevers was used to explore the natural mechanical response of a flexible KAPTON cantilever coated with PVDF-TrFE of different concentrations, and with different solvent formations. It is found that the mechanical response of the PVDF-TrFE coated KAPTON cantilever has reduced vibration amplitude when a combined Methyl Isobutyl Ketone (MIBK) and Dimethyl Sulfoxide (DMSO) is used, but it is not affected with only MIBK is used. When using a combined MIBK and DMSO solvent, the 1.25%w/v PVDF-TrFE material was easily mixed, and it possessed a higher piezoelectric electrical response to the MIBK solutions. The piezoelectrical coefficients were also calculated by applying a dynamic force to the cantilevers and found that q31 of cantilever coated with the PVDF formed using the mixture of DMSO and MIBK solution is higher than that formed using MIBK.
Efficient simultaneous removal of diesel particulate matter and hydrocarbons from diesel exhaust gas at low temperatures over Cu–CeO2/Al2O3 coupling with dielectric barrier discharge plasma
Authors: REN 任 Baoyong 保勇 , FANG 方 Shiyu 世玉 , ZHANG 张 Tiantian 甜甜 , SUN 孙 Yan 燕 , GAO 高 Erhao 尔豪 , LI 李 Jing 晶 , WU 吴 Zuliang 祖良 , ZHU 朱 Jiali 佳丽 , WANG 王 Wei 伟 , YAO 姚 Shuiliang 水良
Published: December 2023

Diesel particulate matter (DPM) and hydrocarbons (HCs) emitted from diesel engines have a negative affect on air quality and human health. Catalysts for oxidative removal of DPM and HCs are currently used universally but their low removal efficiency at low temperatures is a problem. In this study, Cu-doped CeO2 loaded on Al2O3 coupled with plasma was used to enhance low-temperature oxidation of DPM and HCs. Removals of DPM and HCs at 200 °C using the catalyst were as high as 90% with plasma but below 30% without plasma. Operando plasma diffuse reflectance infrared Fourier transform spectroscopy coupled with mass spectrometry was conducted to reveal the functional mechanism of the oxygen species in the DPM oxidation process. It was found that Cu–CeO2 can promote the formation of adsorbed oxygen (

–

) and terminal oxygen (M=O), which can react with DPM to form carbonates that are easily converted to gaseous CO2. Our results provide a practical plasma catalysis technology to obtain simultaneous removals of DPM and HCs at low temperatures.
Rail industry knowledge, experience and perceptions on the use of nature-based solutions as climate change adaptation measures in Australia and the United Kingdom
Authors: Blackwood Lorraine , Renaud Fabrice G , Gillespie Steven
Published: December 2023

Nature-based solutions (NbS) have been identified as sustainable adaptation measures which could be applied to rail infrastructure in response to the impacts of climate change whilst also providing highly valued co-benefits. To date, however, only a limited number of examples of their use have been found in rail, and there has been little investigation into barriers to their uptake. We use an online questionnaire to examine rail industry professionals’ knowledge, experience and thoughts in relation to perceived and/or actual obstacles to the use of NbS as climate change adaptation (CCA) measures for railways, and establish what could aid their wider implementation. This research confirms multiple examples of NbS being used in rail which are not included in the literature, and identifies a lack of awareness of NbS as the largest perceived barrier to their uptake. Education on and promotion of NbS in the industry will therefore be key to its successful widespread deployment. Policy, standards, and client specification were viewed as the best vehicles to enable greater NbS uptake; rail NbS case studies are therefore recommended as means of gathering robust evidence and examples to inform the development of these instruments. Demonstration sites could be used to inform rail stakeholders and communities to garner wider support for the concept. These may also be valuable to the work of researchers and practitioners investigating the wider development and deployment of NbS as sustainable CCA measures across wider (non-rail) sectors and scenarios.
The symmetry regained
Authors: Lo Tien-Chun
Published: December 2023

Collin (2022) attempts to break the symmetry between the modal ontological argument for the existence of God and the reverse modal ontological argument against the existence of God by drawing on some Kripkean lessons about a posteriori necessity. He argues that there is an undercutting defeater for taking God’s non-existence to be possible. In this paper, I reply that taking the Kripkean considerations about a posteriori necessity into account does not help break the symmetry. For we can argue in a similar way that there is an undercutting defeater for taking God’s existence to be possible.
Test–Retest Reliability of Common Behavioral Decision-Making Tasks: A Multi-Sample, Repeated Measures Study
Authors: Buelow Melissa T , Kowalsky Jennifer M , Okdie Bradley M
Published: December 2023

Objective

Decision-making is responsible for the best and worst of human nature. The field of decision science has done much to elucidate the psychological process of decision-making, variables that affect decision-making, and outcomes of disadvantageous decision-making. However, understanding any psychological process requires creation of reliable measures. Few studies focus on the test–retest reliability of behavioral decision-making tasks despite their utility in repeated assessment batteries.

Method

The present study examined the extent to which common behavioral decision-making tasks are reliable across time. Across two samples and two time points, participants completed multiple decision-making assessments.

Results

Results revealed moderate at best evidence of test–retest reliability across a 10-week interval in any of the tasks assessed.

Conclusions

These findings raise large questions for the field of behavioral decision-making and the utility for tasks to track changes in decision-making across time in clinical populations.
Does the Surgical Margin Affect Sexual Function Following Linear Labiaplasty Technique?
Authors: Dogan Ozan , Ucar Elif , Yassa Murat
Published: December 2023

Background

How much labial tissue should be left after labiaplasty is a controversial issue.

Objectives

The objective was to investigate the effect of residual labial tissue following labiaplasty operations on sexual function.

Methods

A total of 150 females who underwent labiaplasty between 2019 and 2021 and their partners were included in the study. In this retrospective study, linear labiaplasty technique was applied according to the patient's request. Patients were either below 1 cm or above 1 cm according to the remaining labial width at follow-up. The remaining labial tissues were classified according to the Motakef classification. Patients with a labial width above 1 cm were included in Group 1, and patients with a labial width below 1 cm were included in Group 2. Sexual function, sexual experience, body image, and erectile function of their partners were compared preoperatively and 2 years postoperatively with appropriate questionnaires.

Results

Sexual function, sexual experience, and body image of females improved in all patients. However, the improvement was more apparent with with remaining labial tissue of greater than 1 cm. The increase in the survey results of the partners was found to be similar.

Conclusions

The sexual function of the patients was better when the width of the labium was longer than 1 cm. This may be due to better protection of the neurovascular structures. This favorable effect was also seen in the subjective evaluation of the partners.

Level of Evidence: 3
Clustering malignant cell states using universally variable genes
Authors: Yoon Sang-Ho , Nam Jin-Wu
Published: December 2023

Single-cell RNA sequencing (scRNA-seq) has revealed important insights into the heterogeneity of malignant cells. However, sample-specific genomic alterations often confound such analysis, resulting in patient-specific clusters that are difficult to interpret. Here, we present a novel approach to address the issue. By normalizing gene expression variances to identify universally variable genes (UVGs), we were able to reduce the formation of sample-specific clusters and identify underlying molecular hallmarks in malignant cells. In contrast to highly variable genes vulnerable to a specific sample bias, UVGs led to better detection of clusters corresponding to distinct malignant cell states. Our results demonstrate the utility of this approach for analyzing scRNA-seq data and suggest avenues for further exploration of malignant cell heterogeneity.
Applying a novel kinomics approach to study decidualization and the effects of antigestagens using a canine model
Authors: De Geyter Isabelle , Kowalewski Mariusz P , Tavares Pereira Miguel
Published: December 2023

Maternal decidual cells are crucial for the maintenance of canine pregnancy as they are the only cells expressing the nuclear progesterone (P4) receptor (PGR) in the placenta. Interfering with P4/PGR signaling adversely affects decidual cells and terminates pregnancy. Although immortalized dog uterine stromal (DUS) cells can be decidualized in vitro using cAMP, the involvement of cAMP-dependent kinases in canine decidualization had not been investigated. Therefore, the present project investigated changes in the kinome of DUS cells following in vitro decidualization, using the serine/threonine kinase (STK) PamChip assay (PamGene). Decidualization led to a predicted activation of 85 STKs in DUS cells, including protein kinase (PK) A, PKC, extracellular signal-regulated kinase (ERK)1/2 and other mitogen-activated protein kinases (MAPKs), calcium/calmodulin-dependent protein kinases (CAMKs), and Akt1/2. In addition, blocking PGR with type 2 antigestagens (aglepristone or mifepristone) decreased the activity of virtually all kinases modulated by decidualization. The underlying transcriptional effects were inferred from comparison with available transcriptomic data on antigestagen-mediated effects in DUS cells. In targeted studies, interfering with PKA or MAPK kinase (MEK)1/2 resulted in downregulation of important decidualization markers (e.g., insulin-like growth factor 1 (IGF1), prostaglandin E2 synthase (PTGES), prolactin receptor (PRLR), PGR, and prostaglandin-endoperoxide synthase 2 (PTGS2/COX2)). Conversely, blocking of PKC decreased the mRNA availability of IGF1, PGR, and PTGS2, but not of PTGES and PRLR. Moreover, suppressing PKA decreased the phosphorylation of the transcription factors cJUN and CREB, whereas blocking of PKC affected only cJUN. This first kinomics analysis to target decidualization showed an increased activity of a wide range of STKs, which could be hindered by disrupting P4/PGR signaling. Decidualization appears to be regulated in a kinase-dependent manner, with PKA and PKC evoking different effects.
Drought experiments need to incorporate atmospheric drying to better simulate climate change
Authors: Wright Alexandra J , Collins Scott L
Published: December 2023

Climate models predict more frequent, prolonged, and extreme droughts in the future. Therefore, drought experiments varying in amount and duration across a range of biogeographical scenarios provide a powerful tool for estimating how drought will affect future ecosystems. Past experimental work has been focused on the manipulation of meteorological drought: Rainout shelters are used to reduce precipitation inputs into the soil. This work has been instrumental in our ability to predict the expected effects of altered rainfall. But what about the nonrainfall components of drought? We review recent literature on the co-occurring and sometimes divergent impacts of atmospheric drying and meteorological drying. We discuss how manipulating meteorological drought or rainfall alone may not predict future changes in plant productivity, composition, or species interactions that result from climate change induced droughts. We make recommendations for how to improve these experiments using manipulations of relative humidity.
The new missense G376V-TDP-43 variant induces late-onset distal myopathy but not amyotrophic lateral sclerosis
Authors: Zibold Julia , Lessard Lola E R , Picard Flavien , da Silva Lara Gruijs , Zadorozhna Yelyzaveta , Streichenberger Nathalie , Belotti Edwige , Osseni Alexis , Emerit Andréa , Errazuriz-Cerda Elisabeth , Michel-Calemard Laurence , Menassa Rita , Coudert Laurent , Wiessner Manuela , Stucka Rolf , Klopstock Thomas , Simonetti Francesca , Hutten Saskia , Nonaka Takashi , Hasegawa Masato , Strom Tim M , Bernard Emilien , Ollagnon Elisabeth , Urtizberea Andoni , Dormann Dorothee , Petiot Philippe , Schaeffer Laurent , Senderek Jan , Leblanc Pascal
Published: December 2023

TAR DNA binding protein of 43 kDa (TDP-43)-positive inclusions in neurons are a hallmark of several neurodegenerative diseases including familial amyotrophic lateral sclerosis (fALS) caused by pathogenic TARDBP variants as well as more common non-Mendelian sporadic ALS (sALS). Here we report a G376V-TDP-43 missense variant in the C-terminal prion-like domain of the protein in two French families affected by an autosomal dominant myopathy but not fulfilling diagnostic criteria for ALS.

Patients from both families presented with progressive weakness and atrophy of distal muscles, starting in their fifth to seventh decade. Muscle biopsies revealed a degenerative myopathy characterized by accumulation of rimmed (autophagic) vacuoles, disruption of sarcomere integrity and severe myofibrillar disorganization. The G376V variant altered a highly conserved amino acid residue and was absent in databases on human genome variation. Variant pathogenicity was supported by in silico analyses and functional studies.

The G376V mutant increased the formation of cytoplasmic TDP-43 condensates in cell culture models, promoted assembly into high molecular weight oligomers and aggregates in vitro, and altered morphology of TDP-43 condensates arising from phase separation. Moreover, the variant led to the formation of cytoplasmic TDP-43 condensates in patient-derived myoblasts and induced abnormal mRNA splicing in patient muscle tissue.

The identification of individuals with TDP-43-related myopathy, but not ALS, implies that TARDBP missense variants may have more pleiotropic effects than previously anticipated and support a primary role for TDP-43 in skeletal muscle pathophysiology. We propose to include TARDBP screening in the genetic work-up of patients with late-onset distal myopathy. Further research is warranted to examine the precise pathogenic mechanisms of TARDBP variants causing either a neurodegenerative or myopathic phenotype.
PAK2 is necessary for myelination in the peripheral nervous system
Authors: Hu Bo , Moiseev Daniel , Schena Isabella , Faezov Bulat , Dunbrack Roland , Chernoff Jonathan , Li Jun
Published: December 2023

Myelination enables electrical impulses to propagate on axons at the highest speed, encoding essential life functions. The Rho family GTPases, RAC1 and CDC42, have been shown to critically regulate Schwann cell myelination. P21-activated kinase 2 (PAK2) is an effector of RAC1/CDC42, but its specific role in myelination remains undetermined. We produced a Schwann cell-specific knockout mouse of Pak2 (scPak2−/−) to evaluate PAK2’s role in myelination.

Deletion of Pak2, specifically in mouse Schwann cells, resulted in severe hypomyelination, slowed nerve conduction velocity and behaviour dysfunctions in the scPak2−/− peripheral nerve. Many Schwann cells in scPak2−/− sciatic nerves were arrested at the stage of axonal sorting. These abnormalities were rescued by reintroducing Pak2, but not the kinase-dead mutation of Pak2, via lentivirus delivery to scPak2−/− Schwann cells in vivo. Moreover, ablation of Pak2 in Schwann cells blocked the promyelinating effect driven by neuregulin-1, prion protein and inactivated RAC1/CDC42. Conversely, the ablation of Pak2 in neurons exhibited no phenotype. Such PAK2 activity can also be either enhanced or inhibited by different myelin lipids.

We have identified a novel promyelinating factor, PAK2, that acts as a critical convergence point for multiple promyelinating signalling pathways. The promyelination by PAK2 is Schwann cell-autonomous. Myelin lipids, identified as inhibitors or activators of PAK2, may be utilized to develop therapies for repairing abnormal myelin in peripheral neuropathies.
‘Dance against the void’: Derek Jarman, dance, queer classical receptions
Authors: Bell Marcus
Published: December 2023

This article considers three moments from the beginning, middle and end of Derek Jarman’s artistic career: Lindsay Kemp’s opening dance in Sebastiane (1976), Jarman’s words on a performance by Michael Clark in the 1980s, and Jarman’s last film Blue (1993), while holding onto the affective registers of his final diary entry (1994). Considering the ways in which Jarman indexed the ephemeral myth-making processes of queer life and art, the author develops a new kinetic-temporal methodology for exploring reception based on the fleeting queer modalities of dance. As such this article makes a series of important connections between classical reception studies, queer theory, critical theory, and dance studies. It argues that, despite the fleeting, erotic, and partial engagements with the past offered by Jarman — which challenge ideas of fixity or lineage — an identification nevertheless emerges with the hierarchies of white supremacist imperialism.
Measuring speech intelligibility with deaf and hard-of-hearing children: A systematic review
Authors: Stefánsdóttir Harpa , Crowe Kathryn , Magnússon Egill , Guiberson Mark , Másdóttir Thora , Ágústsdóttir Inga , Baldursdóttir Ösp V
Published: December 2023

There is great variability in the ways in which the speech intelligibility of d/Deaf and hard-of-hearing (DHH) children who use spoken language as part, or all, of their communication system is measured. This systematic review examined the measures and methods that have been used when examining the speech intelligibility of children who are DHH and the characteristics of these measures and methods. A systematic database search was conducted of CENTRAL; CINAHL; Cochrane; ERIC; Joanna Briggs; Linguistics, Language and Behavior Abstracts; Medline; Scopus; and Web of Science databases, as well as supplemental searches. A total of 204 included studies reported the use of many different measures/methods which measured segmental aspects of speech, with the most common being Allen et al.’s (2001, The reliability of a rating scale for measuring speech intelligibility following pediatric cochlear implantation. Otology and Neurotology, 22(5), 631-633. https://doi.org/10.1097/00129492-200109000-00012) Speech Intelligibility Rating scale. Many studies included insufficient details to determine the measure that was used. Future research should utilize methods/measures with known psychometric validity, provide clear descriptions of the methods/measures used, and consider using more than one measure to account for limitations inherent in different methods of measuring the speech intelligibility of children who are DHH, and consider and discuss the rationale for the measure/method chosen.
Leftover liquids and the moisture of mourning: the oozes of Ocean Vuong’s oeuvre
Authors: Vu Minh Huynh
Published: December 2023

This article tracks the moisture that spills across Ocean Vuong’s poetry and prose. Whereas the oceanic serves as the spectacular site across which Vietnamese refugees are rescued and rehabilitated through the scripts of US humanitarianism, moisture – as an ambient material and process – coagulates a queer, minor mode of refugee mourning and melancholia in the ongoing aftermath of the War in Vietnam. Pooling together these leftover liquids – sweat, mud, blood, amniotic fluid, semen, and urine – this study considers how the literary and chemical properties of humidity can alter extant epistemic configurations of war: not as an exceptional event, but instead as an everyday surround that continues to be weathered.
Development of deep-learning models for real-time anaerobic threshold and peak VO2 prediction during cardiopulmonary exercise testing
Authors: Watanabe Tatsuya , Tohyama Takeshi , Ikeda Masataka , Fujino Takeo , Hashimoto Toru , Matsushima Shouji , Kishimoto Junji , Todaka Koji , Kinugawa Shintaro , Tsutsui Hiroyuki , Ide Tomomi
Published: December 2023

Aims

Exercise intolerance is a clinical feature of patients with heart failure (HF). Cardiopulmonary exercise testing (CPET) is the first-line examination for assessing exercise capacity in patients with HF. However, the need for extensive experience in assessing anaerobic threshold (AT) and the potential risk associated with the excessive exercise load when measuring peak oxygen uptake (peak VO2) limit the utility of CPET. This study aimed to use deep-learning approaches to identify AT in real time during testing (defined as real-time AT) and to predict peak VO2 at real-time AT.

Methods and results

This study included the time-series data of CPET recorded at the Department of Cardiovascular Medicine, Kyushu University Hospital. Two deep neural network models were developed to: (i) estimate the AT probability using breath-by-breath data and (ii) predict peak VO2 using the data at the real-time AT. The eligible CPET contained 1472 records of 1053 participants aged 18–90 years and 20% were used for model evaluation. The developed model identified real-time AT with 0.82 for correlation coefficient (Corr) and 1.20 mL/kg/min for mean absolute error (MAE), and the corresponding AT time with 0.86 for Corr and 0.66 min for MAE. The peak VO2 prediction model achieved 0.87 for Corr and 2.25 mL/kg/min for MAE.

Conclusion

Deep-learning models for real-time CPET analysis can accurately identify AT and predict peak VO2. The developed models can be a competent assistant system to assess a patient’s condition in real time, expanding CPET utility.
Co-exposure to multiple air pollutants, genetic susceptibility, and the risk of myocardial infarction onset: a cohort analysis of the UK Biobank participants
Authors: Jiang Zhou , Zhang Shuo , Gao Tongyu , Chen Keying , Liu Yuxin , Liu Ying , Wang Ting , Zeng Ping
Published: December 2023

Aims

The relationship between the long-term joint exposure to ambient air pollution and incidence of myocardial infarction (MI) and modification by genetic susceptibility remain inconclusive.

Methods and results

We analysed 329 189 UK Biobank participants without MI at baseline. Exposure concentrations to particulate matter (PM2.5 and PM10), nitrogen dioxide (NO2), and nitrogen oxides (NOx) were obtained. Air pollution score assessing the joint exposure was calculated, and its association with MI was evaluated via Cox model under the P value aggregation framework. Genetic susceptibility to MI was evaluated by incorporating polygenic risk score (PRS) into models. Risk prediction models were also established. During a median follow-up of 13.4 years, 9993 participants developed MI. Per interquartile range increase of PM2.5, PM10, NO2, and NOx resulted in 74% [95% confidence intervals (CIs) 69%–79%], 67% (63%–72%), 46% (42%–49%), and 38% (35%–41%) higher risk of MI. Compared with the lowest quartile (Q1) of air pollution score, the multivariable adjusted hazard ratio (HR) (95%CIs) of Q4 (the highest cumulative air pollution) was 3.50 (3.29–3.72) for MI. Participants with the highest PRS and air pollution score possessed the highest risk of incident MI (HR = 4.88, 95%CIs 4.35–5.47). Integrating PRS, air pollution exposure, and traditional factors substantially improved risk prediction of MI.

Conclusion

Long-term joint exposure to air pollutants including PM2.5, PM10, NO2, and NOx is substantially associated with increased risk of MI. Genetic susceptibility to MI strengthens such adverse joint association. Air pollutions together with genetic and traditional factors enhance the accuracy of MI risk prediction.
A native phosphoglycolate salvage pathway of the synthetic autotrophic yeast Komagataella phaffii
Authors: Baumschabl Michael , Mitic Bernd M , Troyer Christina , Hann Stephan , Ata Özge , Mattanovich Diethard
Published: December 2023

Synthetic autotrophs can serve as chassis strains for bioproduction from CO2 as a feedstock to take measures against the climate crisis. Integration of the Calvin–Benson–Bassham (CBB) cycle into the methylotrophic yeast Komagataella phaffii (Pichia pastoris) enabled it to use CO2 as the sole carbon source. The key enzyme in this cycle is ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzing the carboxylation step. However, this enzyme is error prone to perform an oxygenation reaction leading to the production of toxic 2-phosphoglycolate. Native autotrophs have evolved different recycling pathways for 2-phosphoglycolate. However, for synthetic autotrophs, no information is available for the existence of such pathways. Deletion of CYB2 in the autotrophic K. phaffii strain led to the accumulation of glycolate, an intermediate in phosphoglycolate salvage pathways, suggesting that such a pathway is enabled by native K. phaffii enzymes. 13C tracer analysis with labeled glycolate indicated that the yeast pathway recycling phosphoglycolate is similar to the plant salvage pathway. This orthogonal yeast pathway may serve as a sensor for RuBisCO oxygenation, and as an engineering target to boost autotrophic growth rates in K. phaffii.
Proportion of Nonindustrial Private Forest Lands That Potentially Can Be Leased to Bioenergy Enterprises to Grow Short Rotation Woody Crops
Authors: Hussain Anwar , Munn Ian A , Grala Robert K
Published: December 2023

Determining how much nonindustrial private forest (NIPF) land could potentially be allocated to growing short rotation woody crops (SRWCs) is critical for estimating the future supply of woody biomass for biofuels and overall bioenergy production. This study estimated the proportion of the land NIPF landowners would be willing to allocate to SRWC cultivation. In view of the bounded nature of the dependent binary variable [0,1] and model performance, a fractional logit regression model was used to estimate model parameters. The estimated proportion of land allocated to SRWCs was positively influenced by the rental rate per acre, owning land for investment or fee-access hunting purposes, and the landowner’s age. In contrast, size of the ownership, owning land for the production of agricultural products, and residing on the land negatively influenced the proportion of land allocated to SRWCs. Lease contract duration, location of the largest tract owned, owning land for personal recreation or ecosystem services, and landowner familiarity with the concept of alternative fuels production did not influence the proportion of land allocated to SRWCs. These results will contribute to a better understanding of SRWC biomass supply from NIPF land and provide important benchmark information for conducting feasibility analyses of biofuel and biopower manufacturing in Mississippi and other states with abundant woody feedstocks.

Study Implications: To achieve targeted levels of bioenergy production and carbon dioxide (CO2) emission reductions and diversify NIPF landowner income, participation of NIPF landowners in woody biomass feedstock production will be critical, because they own a majority of forestland in the region. Moreover, they have diverse reasons for owning land which has extensive implications not only in terms of incentive types or monetary compensation levels they might require for cultivating SRWCs but also policies related to the development of the bioenergy sector in Mississippi, the location of individual bioenergy processing facilities, and feedstock types that will be developed. Thus, forest managers and biomass procurement foresters might need to decide whether to focus their efforts on maximizing the land area allocated to growing SRWCs or considering a mix of SRWCs at lower lease rates per acre and material obtained from thinnings, which might be more amenable to landowners who value environmental amenities.
Leaping through Tree Space: Continuous Phylogenetic Inference for Rooted and Unrooted Trees
Authors: Penn Matthew J , Scheidwasser Neil , Penn Joseph , Donnelly Christl A , Duchêne David A , Bhatt Samir
Published: December 2023

Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains challenging. To address this problem, for the first time, we perform both tree exploration and inference in a continuous space where the computation of gradients is possible. This continuous relaxation allows for major leaps across tree space in both rooted and unrooted trees, and is less susceptible to convergence to local minima. Our approach outperforms the current best methods for inference on unrooted trees and, in simulation, accurately infers the tree and root in ultrametric cases. The approach is effective in cases of empirical data with negligible amounts of data, which we demonstrate on the phylogeny of jawed vertebrates. Indeed, only a few genes with an ultrametric signal were generally sufficient for resolving the major lineages of vertebrates. Optimization is possible via automatic differentiation and our method presents an effective way forward for exploring the most difficult, data-deficient phylogenetic questions.
Patchwork: Alignment-Based Retrieval and Concatenation of Phylogenetic Markers from Genomic Data
Authors: Thalén Felix , Köhne Clara G , Bleidorn Christoph
Published: December 2023

Low-coverage whole-genome sequencing (also known as “genome skimming”) is becoming an increasingly affordable approach to large-scale phylogenetic analyses. While already routinely used to recover organellar genomes, genome skimming is rather rarely utilized for recovering single-copy nuclear markers. One reason might be that only few tools exist to work with this data type within a phylogenomic context, especially to deal with fragmented genome assemblies. We here present a new software tool called Patchwork for mining phylogenetic markers from highly fragmented short-read assemblies as well as directly from sequence reads. Patchwork is an alignment-based tool that utilizes the sequence aligner DIAMOND and is written in the programming language Julia. Homologous regions are obtained via a sequence similarity search, followed by a “hit stitching” phase, in which adjacent or overlapping regions are merged into a single unit. The novel sliding window algorithm trims away any noncoding regions from the resulting sequence. We demonstrate the utility of Patchwork by recovering near-universal single-copy orthologs within a benchmarking study, and we additionally assess the performance of Patchwork in comparison with other programs. We find that Patchwork allows for accurate retrieval of (putatively) single-copy genes from genome skimming data sets at different sequencing depths with high computational speed, outperforming existing software targeting similar tasks. Patchwork is released under the GNU General Public License version 3. Installation instructions, additional documentation, and the source code itself are all available via GitHub at https://github.com/fethalen/Patchwork.
Opportunistic Bacteria of Grapevine Crown Galls Are Equipped with the Genomic Repertoire for Opine Utilization
Authors: Faist Hanna , Ankenbrand Markus J , Sickel Wiebke , Hentschel Ute , Keller Alexander , Deeken Rosalia
Published: December 2023

Young grapevines (Vitis vinifera) suffer and eventually can die from the crown gall disease caused by the plant pathogen Allorhizobium vitis (Rhizobiaceae). Virulent members of A. vitis harbor a tumor-inducing plasmid and induce formation of crown galls due to the oncogenes encoded on the transfer DNA. The expression of oncogenes in transformed host cells induces unregulated cell proliferation and metabolic and physiological changes. The crown gall produces opines uncommon to plants, which provide an important nutrient source for A. vitis harboring opine catabolism enzymes. Crown galls host a distinct bacterial community, and the mechanisms establishing a crown gall–specific bacterial community are currently unknown. Thus, we were interested in whether genes homologous to those of the tumor-inducing plasmid coexist in the genomes of the microbial species coexisting in crown galls. We isolated 8 bacterial strains from grapevine crown galls, sequenced their genomes, and tested their virulence and opine utilization ability in bioassays. In addition, the 8 genome sequences were compared with 34 published bacterial genomes, including closely related plant-associated bacteria not from crown galls. Homologous genes for virulence and opine anabolism were only present in the virulent Rhizobiaceae. In contrast, homologs of the opine catabolism genes were present in all strains including the nonvirulent members of the Rhizobiaceae and non-Rhizobiaceae. Gene neighborhood and sequence identity of the opine degradation cluster of virulent and nonvirulent strains together with the results of the opine utilization assay support the important role of opine utilization for cocolonization in crown galls, thereby shaping the crown gall community.
Using encrypted genotypes and phenotypes for collaborative genomic analyses to maintain data confidentiality
Authors: Zhao Tianjing , Wang Fangyi , Mott Richard , Dekkers Jack , Cheng Hao
Published: December 2023

To adhere to and capitalize on the benefits of the FAIR (findable, accessible, interoperable, and reusable) principles in agricultural genome-to-phenome studies, it is crucial to address privacy and intellectual property issues that prevent sharing and reuse of data in research and industry. Direct sharing of genotype and phenotype data is often prohibited due to intellectual property and privacy concerns. Thus, there is a pressing need for encryption methods that obscure confidential aspects of the data, without affecting the outcomes of certain statistical analyses. A homomorphic encryption method for genotypes and phenotypes (HEGP) has been proposed for single-marker regression in genome-wide association studies (GWAS) using linear mixed models with Gaussian errors. This methodology permits frequentist likelihood-based parameter estimation and inference. In this paper, we extend HEGP to broader applications in genome-to-phenome analyses. We show that HEGP is suited to commonly used linear mixed models for genetic analyses of quantitative traits including genomic best linear unbiased prediction (GBLUP) and ridge-regression best linear unbiased prediction (RR-BLUP), as well as Bayesian variable selection methods (e.g. those in Bayesian Alphabet), for genetic parameter estimation, genomic prediction, and GWAS. By advancing the capabilities of HEGP, we offer researchers and industry professionals a secure and efficient approach for collaborative genomic analyses while preserving data confidentiality.
Returning personalized, genetic health test results to individuals of African descent or ancestry in precision medicine research
Authors: Hendricks-Sturrup Rachele M , Emmott Nora , Nafie Maryam , Edgar Lauren , Johnson-Glover Tracey , Christensen Kurt D , Argetsinger Stephanie , Lu Christine Y
Published: December 2023

Today, many epidemiological studies and biobanks are offering to disclose individual genetic results to their participants, including the National Institutes of Health's All of Us Research Program. Returning hereditary disease risks and pharmacogenetic test results to study participants from racial/ethnic groups that are historically underrepresented in biomedical research poses specific challenges to those participants and the health system writ large. For example, individuals of African descent are underrepresented in research about drug–gene interactions and have a relatively higher proportion of variants of unknown significance, affecting their ability to take clinical action following return of results. In this brief report, we summarize studies published to date concerning the perspectives and/or attitudes of African Americans engaged in genetic research programs to anticipate factors in disclosure protocols that would minimize risks and maximize benefits. A thematic analysis of studies identified (n = 6) lends to themes centered on motivations to engage or disengage in the return of results and integrating research and care. Actionable strategies determined in reaction to these themes center on ensuring adequate system and health education support for participants and personalizing the process for participants engaging in return of results. Overall, we offer these themes and actionable strategies as early guidance to research programs, and provide recommendations to policy makers focused on fair and equitable return of genetic research results to underrepresented research participants.
Populus cathayana genome and population resequencing provide insights into its evolution and adaptation
Authors: Xiang Xiaodong , Zhou Xinglu , Zi Hailing , Wei Hantian , Cao Demei , Zhang Yahong , Zhang Lei , Hu Jianjun
Published: December 2023

Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55 Mb (scaffold N50 = 20.86 Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype–environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.
Quantifying income inequality in years of life lost to COVID-19: a prediction model approach using Dutch administrative data
Authors: Issa Jawa , Wouterse Bram , Milkovska Elena , van Baal Pieter
Published: December 2023

Background

Low socioeconomic status and underlying health increase the risk of fatal outcomes from COVID-19, resulting in more years of life lost (YLL) among the poor. However, using standard life expectancy overestimates YLL to COVID-19. We aimed to quantify YLL associated with COVID-19 deaths by sex and income quartile, while accounting for the impact of individual-level pre-existing health on remaining life expectancy for all Dutch adults aged 50+.

Methods

Extensive administrative data were used to model probability of dying within the year for the entire 50+ population in 2019, considering age, sex, disposable income and health care use (n = 6 885 958). The model is used to predict mortality probabilities for those who died of COVID-19 (had they not died) in 2020. Combining these probabilities in life tables, we estimated YLL by sex and income quartile. The estimates are compared with YLL based on standard life expectancy and income-stratified life expectancy.

Results

Using standard life expectancy results in 167 315 YLL (8.4 YLL per death) which is comparable to estimates using income-stratified life tables (167 916 YLL with 8.2 YLL per death). Considering pre-existing health and income, YLL decreased to 100 743, with 40% of years lost in the poorest income quartile (5.0 YLL per death). Despite individuals in the poorest quartile dying at younger ages, there were minimal differences in average YLL per COVID-19 death compared with the richest quartile.

Conclusions

Accounting for prior health significantly affects estimates of YLL due to COVID-19. However, inequality in YLL at the population level is primarily driven by higher COVID-19 deaths among the poor. To reduce income inequality in the health burden of future pandemics, policies should focus on limiting structural differences in underlying health and exposure of lower income groups.
Strategies to overcome low MHC-I expression in paediatric and adult tumours
Authors: Guillaume J , Perzolli A , Boes M
Published: December 2023

Immunotherapy has made significant advancements in cancer treatments, improving patients’ survival rates and quality of life. Several challenges still need to be addressed, which include the considerable fraction of incomplete curative responses in cancer patients, the development of therapy resistance by tumours, and the occurrence of adverse effects, such as inflammatory and autoimmune complications. Paediatric tumours usually exhibit lower responsiveness to immunotherapies compared to adult tumours. Although the underlying reasons are not yet fully understood, one known mechanism by which tumours avoid immune recognition is through reduced cell surface expression of major histocompatibility complex class I (MHC-I) complexes. Accordingly, the reduced presentation of neoantigens by MHC-I hinders the recognition and targeting of tumour cells by CD8+ T cells, impeding T-cell-mediated cytotoxic anti-tumour responses. MHC-I downregulation indeed often correlates with a poorer prognosis and diminished response to immunotherapy. Understanding the mechanisms underlying MHC-I downregulation in different types of paediatric and adult tumours is crucial for developing strategies to restore MHC-I expression and enhance anti-tumour immune responses. We here discuss progress in MHC-I-based immunotherapies against cancers.