bluuebunny/crossref_metadata_2025 huggingface dataset:
A curated census of pathogenic and likely pathogenic UTR variants and evaluation of deep learning models for variant effect prediction
Authors: Bohn Emma , Lau Tammy T. Y. , Wagih Omar , Masud Tehmina , Merico Daniele
Published: September 2023

Introduction: Variants in 5′ and 3′ untranslated regions (UTR) contribute to rare disease. While predictive algorithms to assist in classifying pathogenicity can potentially be highly valuable, the utility of these tools is often unclear, as it depends on carefully selected training and validation conditions. To address this, we developed a high confidence set of pathogenic (P) and likely pathogenic (LP) variants and assessed deep learning (DL) models for predicting their molecular effects.

Methods: 3′ and 5′ UTR variants documented as P or LP (P/LP) were obtained from ClinVar and refined by reviewing the annotated variant effect and reassessing evidence of pathogenicity following published guidelines. Prediction scores from sequence-based DL models were compared between three groups: P/LP variants acting though the mechanism for which the model was designed (model-matched), those operating through other mechanisms (model-mismatched), and putative benign variants. PhyloP was used to compare conservation scores between P/LP and putative benign variants.

Results: 295 3′ and 188 5′ UTR variants were obtained from ClinVar, of which 26 3′ and 68 5′ UTR variants were classified as P/LP. Predictions by DL models achieved statistically significant differences when comparing modelmatched P/LP variants to both putative benign variants and modelmismatched P/LP variants, as well as when comparing all P/LP variants to putative benign variants. PhyloP conservation scores were significantly higher among P/LP compared to putative benign variants for both the 3′ and 5′ UTR.

Discussion: In conclusion, we present a high-confidence set of P/LP 3′ and 5′ UTR variants spanning a range of mechanisms and supported by detailed pathogenicity and molecular mechanism evidence curation. Predictions from DL models further substantiate these classifications. These datasets will support further development and validation of DL algorithms designed to predict the functional impact of variants that may be implicated in rare disease.
BACE1 and SCD1 are associated with neurodegeneration
Authors: Bedoya-Guzmán Ferley A. , Pacheco-Herrero Mar , Salomon-Cruz Ivan Daniel , Barrera-Sandoval Angela Maria , Gutierrez Vargas Johanna Andrea , Villamil-Ortiz Javier Gustavo , Villegas Lanau Carlos Andres , Arias-Londoño Julián David , Area-Gomez Estela , Cardona Gomez Gloria Patricia
Published: September 2023

Introduction

Proteolytic processing of amyloid protein precursor by β-site secretase enzyme (BACE1) is dependent on the cellular lipid composition and is affected by endomembrane trafficking in dementia and Alzheimer's disease (AD). Stearoyl-CoA desaturase 1 (SCD1) is responsible for the synthesis of fatty acid monounsaturation (MUFAs), whose accumulation is strongly associated with cognitive dysfunction.

Methods

In this study, we analyzed the relationship between BACE1 and SCD1 in vivo and in vitro neurodegenerative models and their association in familial AD (FAD), sporadic AD (SAD), and cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) using microscopy, biochemical, and mass SPECT approach.

Results

Our findings showed that BACE1 and SCD1 immunoreactivities were increased and colocalized in astrocytes of the hippocampus in a rat model of global cerebral ischemia (2-VO). A synergistic effect of double BACE1/SCD1 silencing on the recovery of motor and cognitive functions was obtained. This neuroprotective regulation involved the segregation of phospholipids (PLs) associated with polyunsaturated fatty acids in the hippocampus, cerebrospinal fluid, and serum. The double silencing in the sham and ischemic groups was stronger in the serum, inducing an inverse ratio between total phosphatydilcholine (PC) and lysophosphatidylcholine (LPC), represented mainly by the reduction of PC 38:4 and PC 36:4 and an increase in LPC 16:0 and LPC 18:0. Furthermore, PC 38:4 and PC:36:4 levels augmented in pathological conditions in in vitro AD models. BACE1 and SCD1 increases were confirmed in the hippocampus of FAD, SAD, and CADASIL.

Conclusion

Therefore, the findings suggest a novel convergence of BACE-1 and SCD1 in neurodegeneration, related to pro-inflammatory phospholipids.
CUT homeobox genes: transcriptional regulation of neuronal specification and beyond
Authors: Leyva-Díaz Eduardo
Published: September 2023

CUT homeobox genes represent a captivating gene class fulfilling critical functions in the development and maintenance of multiple cell types across a wide range of organisms. They belong to the larger group of homeobox genes, which encode transcription factors responsible for regulating gene expression patterns during development. CUT homeobox genes exhibit two distinct and conserved DNA binding domains, a homeodomain accompanied by one or more CUT domains. Numerous studies have shown the involvement of CUT homeobox genes in diverse developmental processes such as body axis formation, organogenesis, tissue patterning and neuronal specification. They govern these processes by exerting control over gene expression through their transcriptional regulatory activities, which they accomplish by a combination of classic and unconventional interactions with the DNA. Intriguingly, apart from their roles as transcriptional regulators, they also serve as accessory factors in DNA repair pathways through protein–protein interactions. They are highly conserved across species, highlighting their fundamental importance in developmental biology. Remarkably, evolutionary analysis has revealed that CUT homeobox genes have experienced an extraordinary degree of rearrangements and diversification compared to other classes of homeobox genes, including the emergence of a novel gene family in vertebrates. Investigating the functions and regulatory networks of CUT homeobox genes provides significant understanding into the molecular mechanisms underlying embryonic development and tissue homeostasis. Furthermore, aberrant expression or mutations in CUT homeobox genes have been associated with various human diseases, highlighting their relevance beyond developmental processes. This review will overview the well known roles of CUT homeobox genes in nervous system development, as well as their functions in other tissues across phylogeny.
Characterization of extracellular spike waveforms recorded in wallaby primary visual cortex
Authors: Jung Young Jun , Sun Shi H. , Almasi Ali , Yunzab Molis , Meffin Hamish , Ibbotson Michael R.
Published: September 2023

Extracellular recordings were made from 642 units in the primary visual cortex (V1) of a highly visual marsupial, the Tammar wallaby. The receptive field (RF) characteristics of the cells were objectively estimated using the non-linear input model (NIM), and these were correlated with spike shapes. We found that wallaby cortical units had 68% regular spiking (RS), 12% fast spiking (FS), 4% triphasic spiking (TS), 5% compound spiking (CS) and 11% positive spiking (PS). RS waveforms are most often associated with recordings from pyramidal or spiny stellate cell bodies, suggesting that recordings from these cell types dominate in the wallaby cortex. In wallaby, 70–80% of FS and RS cells had orientation selective RFs and had evenly distributed linear and nonlinear RFs. We found that 47% of wallaby PS units were non-orientation selective and they were dominated by linear RFs. Previous studies suggest that the PS units represent recordings from the axon terminals of non-orientation selective cells originating in the lateral geniculate nucleus (LGN). If this is also true in wallaby, as strongly suggested by their low response latencies and bursty spiking properties, the results suggest that significantly more neurons in wallaby LGN are already orientation selective. In wallaby, less than 10% of recorded spikes had triphasic (TS) or sluggish compound spiking (CS) waveforms. These units had a mixture of orientation selective and non-oriented properties, and their cellular origins remain difficult to classify.
Impact of oncoplasty in increasing breast conservation rates Post neo-adjuvant chemotherapy
Authors: Koppiker Chaitanyanand B. , Kelkar Devaki A. , Kulkarni Madhura , Kadu Shweta , Pai Mugdha , Dhar Upendra , Deshmukh Chetan , Varghese Beenu , Zamre Vaishali , Jumle Nutan , Gangurde Nutan , Joshi Anjali , Unde Rohini , Banale Rituja , Namewar Namrata , Vaid Pooja , Busheri Laleh , Thomas George , Nare Smeeta , Pereira Jerome , Badve Sunil
Published: September 2023

Introduction

The essential goal of neoadjuvant chemotherapy (NACT) is to downstage the primary tumor making it amenable for breast conservation surgery (BCS). However, since the safety of this surgery is paramount, post-NACT breast conservation rates remain low. As per the recommendation of the 2018 Early Breast Cancer Trialists’ Collaborative Group (EBCTCG) overview of long-term post-NACT follow-up, we have devised a protocol for imaging, localization, rad-path analysis, and documentation of radiotherapy techniques to ensure the safety of post-NACT breast conservation.

Methods

This is a retrospective cohort of 180 breast cancer patients who received NACT and were operated on by a single surgical oncologist from 2015 to 2020. After selection based on published guidelines, patients were treated with neoadjuvant systemic (chemo or hormone) therapy. In cases where primary tumors responded and reduced to 1–2 cm in size mid-NACT, the residual tumors were localized by clips under ultrasound guidance and calcification was wire localized. All patients were treated using appropriate surgical and oncoplastic techniques where indicated. Negative margins were ensured by intra-operative rad-path analysis. Adjuvant chemotherapy and radiotherapy were given as per protocol.

Results

In 81 cases that required mastectomy at presentation, we were able to achieve a 72.8% post-NACT BCS rate with the help of oncoplasty. Overall, 142 of 180 (80%) patients were treated with breast conserving surgery of which 80% (121 of 142) were oncoplasty. Margins were assessed on intra-operative frozen and re-excised in the same setting. No positive margins were reported in final histopath of 142 breast conservation procedures. Post-operative complication rates after breast conservation in the first year were at 17% (24 of 142 including two major complications). Patient reported outcomes were satisfactory with increased satisfaction for breast conservation compared with immediate breast reconstruction.

Discussion

Employing oncoplastic breast surgery (OBS) techniques following stringent protocols for accurate localization of the residual tumor, intra-operative rad-path analysis, and adjuvant treatments, we show successful breast conservation in 72.8% of our mastectomy-qualified patients after downstaging by NACT. We also report satisfactory outcomes for post-NACT surgery, patient-reported satisfaction, and survival.
Extracorporeal light-chain elimination in myeloma with simple medium cutoff membrane hemodialysis: a retrospective cohort study
Authors: Schaaf Christian W. , Braunisch Matthias C. , Holzmann-Littig Christopher , Pfister Frederick , Hannemann Liya , Hausinger Renate I. , Verbeek Mareike , Schmaderer Christoph , Renders Lutz , Heemann Uwe , Küchle Claudius
Published: September 2023

Background

We determined the efficacy of free light chain (FLC) removal by regular dialysis equipment (high-flux filtration) with medium cutoff (MCO) membrane hemodialysis (HD) as an adjuvant treatment to standard chemotherapy for patients with acute kidney injury complicating multiple myeloma (MM) and its impact on further dialysis dependency.

Methods

Sixty patients with acute dialysis-dependent renal failure secondary to MM were treated with MCO-HD (55 patients) or HCO (high cutoff)-HD (5 patients) as a control. FLC serum concentration, total protein, immunoglobulins, and LDH were measured throughout the dialysis therapy. The kidney function of the patients was followed up for 1 year.

Results

The median age was 69 years; 25 female and 35 male patients were enrolled. HD significantly reduced FLC kappa levels in the MCO/HCO group by 58%/84% (MCO/HCO group; p < 0.05) and FLC lambda by 39%/33% (MCO/HCO group; p < 0.05). Single HD data (MCO) showed a relative reduction of 70% in kappa and 37% in lambda FLC concentration, as expected by the different sizes of the light chains. Renal function improved significantly and continuously from starting creatinine 5.7/3.8 mg/dl (MCO/HCO group) before HD to 1.4/2.0 mg/dl (MCO/HCO group; p < 0.001) after 1 year. No significant alteration of total protein, immunoglobulins, and LDH concentrations by HD (HCO and MCO group) was observed. After 1 year, 37 of 60 patients were alive and 34 of them were off dialysis.

Conclusion

FLC elimination with MCO-HD is effective, technically easy, and less cost-intensive as compared with HCO-HD. Kidney function recovery in MM patients is achievable.
Mechanism of HBx carcinogenesis interaction with non-coding RNA in hepatocellular carcinoma
Authors: Wang Zhuoran , Li Nan , Cai Peng , Zhang Cunzhen , Cao Guangwen , Yin Jianhua
Published: September 2023

Hepatocellular carcinoma (HCC) is an extremely malignant tumor that affects individuals throughout the world. One of the main causes of HCC is hepatitis B virus (HBV). Therefore, it is crucial to understand the mechanisms underlying HBV carcinogenesis. Increasing evidence suggests that the HBV X protein (HBx), which is encoded by HBV, plays a significant role in cell apoptosis, DNA damage repair, and cell cycle regulation. This ultimately leads to the development of HCC. Additionally, recent studies have shown that non-coding RNA (ncRNA) also contributes to the carcinogenesis and pathogenesis of different of tumors. ncRNA plays a significant role in the formation of HCC by regulating the inflammatory signaling pathway, activating immune cells, and modifying epigenetics. However, it remains unclear whether ncRNA is involved in the regulation of the carcinogenic mechanisms of HBx. This article reviews the carcinogenic mechanism of HBx and its interaction with ncRNA, providing a novel strategy for the clinical diagnosis and treatment of HCC.
CEA-delta could be a biomarker of tumor phenotype, clinical stage, and chemotherapeutic response in rectal cancer with OCT4-positive cancer stem cells
Authors: Lozada-Martinez Ivan David , Bolaño-Romero Maria Paz , Lambis-Anaya Lina , Liscano Yamil , Suarez-Causado Amileth
Published: September 2023

Background

There is very limited evidence on biomarkers for evaluating the clinical behavior and therapeutic response in rectal cancer (RC) with positive expression of cancer stem cells (CSCs).

Methods

An exploratory prospective study was conducted, which included fresh samples of tumor tissue from 109 patients diagnosed with primary RC. Sociodemographic, pathological and clinical characteristics were collected from medical records and survey. The OCT4 protein was isolated using the Western Blot technique. It was calculated the ΔCEA, ΔOCT4, and ΔOCT4/GUSB values by assessing the changes before and after chemotherapy, aiming to evaluate the therapeutic response.

Results

Patients had an average age of 69.9 years, with 55% (n=60) being male. Approximately 63.3% of the tumors were undifferentiated, and the most frequent staging classification was pathological stage III (n=64; 58.7%). Initial positive expression was observed in 77.1% of the patients (n=84), and the median ΔCEA was -1.03 (-3.82 - 0.84) ng/ml, with elevated levels (< -0.94 ng/ml) found in 51.4% of the subjects (n=56). Being OCT4 positive and having an elevated ΔCEA value were significantly associated with undifferentiated tumor phenotype (p=0.002), advanced tumor progression stage (p <0.001), and negative values of ΔOCT4 (p <0.001) (suggestive of poor therapeutic response) compared to those without this status.

Conclusion

This study identified a significant and directly proportional association among the values of ΔCEA, ΔOCT4, and ΔOCT4/GUSB. These findings suggest that ΔCEA holds potential as a clinical biomarker for determining the undifferentiated tumor phenotype, advanced clinical stage, and poor therapeutic response in RC with CSCs positive expression.
Repetitive mild traumatic brain injury-induced neurodegeneration and inflammation is attenuated by acetyl-L-carnitine in a preclinical model
Authors: Hiskens Matthew I. , Li Katy M. , Schneiders Anthony G. , Fenning Andrew S.
Published: September 2023

Repetitive mild traumatic brain injuries (rmTBI) may contribute to the development of neurodegenerative diseases through secondary injury pathways. Acetyl-L-carnitine (ALC) shows neuroprotection through anti-inflammatory effects and via regulation of neuronal synaptic plasticity by counteracting post-trauma excitotoxicity. This study aimed to investigate mechanisms implicated in the etiology of neurodegeneration in rmTBI mice treated with ALC. Adult male C57BL/6J mice were allocated to sham, rmTBI or ALC + rmTBI groups. 15 rmTBIs were administered across 23 days using a modified weight drop model. Neurological testing and spatial learning and memory assessments via the Morris Water Maze (MWM) were undertaken at 48 h and 3 months. RT-PCR analysis of the cortex and hippocampus was undertaken for MAPT, GFAP, AIF1, GRIA, CCL11, TDP43, and TNF genes. Gene expression in the cortex showed elevated mRNA levels of MAPT, TNF, and GFAP in the rmTBI group that were reduced by ALC treatment. In the hippocampus, mRNA expression was elevated for GRIA1 in the rmTBI group but not the ALC + rmTBI treatment group. ALC treatment showed protective effects against the deficits displayed in neurological testing and MWM assessment observed in the rmTBI group. While brain structures display differential vulnerability to insult as evidenced by location specific postimpact disruption of key genes, this study shows correlative mRNA neurodegeneration and functional impairment that was ameliorated by ALC treatment in several key genes. ALC may mitigate damage inflicted in the various secondary neurodegenerative cascades and contribute to functional protection following rmTBI.
Application of cell-derived exosomes in the hematological malignancies therapy
Authors: Ghaffari Kazem , Moradi-Hasanabad Amin , Sobhani-Nasab Ali , Javaheri Javad , Ghasemi Ali
Published: September 2023

Exosomes are small membrane vesicles of endocytic origin that are produced by both tumor and normal cells and can be found in physiological fluids like plasma and cell culture supernatants. They include cytokines, growth factors, proteins, lipids, RNAs, and metabolites and are important intercellular communication controllers in several disorders. According to a vast amount of research, exosomes could support or inhibit tumor start and diffusion in a variety of solid and hematological malignancies by paracrine signaling. Exosomes are crucial therapeutic agents for a variety of illnesses, such as cancer and autoimmune diseases. This review discusses the most current and encouraging findings from in vitro and experimental in vivo research, as well as the scant number of ongoing clinical trials, with a focus on the impact of exosomes in the treatment of malignancies. Exosomes have great promise as carriers of medications, antagonists, genes, and other therapeutic materials that can be incorporated into their core in a variety of ways. Exosomes can also alter the metabolism of cancer cells, alter the activity of immunologic effectors, and alter non-coding RNAs, all of which can alter the tumor microenvironment and turn it from a pro-tumor to an anti-tumor milieu. This subject is covered in the current review, which also looks at how exosomes contribute to the onset and progression of hematological malignancies, as well as their importance in diagnosing and treating these conditions.
Topological polarisation states
Authors: Saito Shinichi
Published: September 2023

Polarisation states are described by spin expectation values, known as Stokes parameters, the trajectories of which in a rotationally symmetric system form a sphere named after Poincaré. Here, we show that the trajectories of broken rotational symmetric systems can exhibit distinct topological structures in polarisation states. We use a phase-shifter to form a polarisation circle(S1), which interferes with the original input due to the phase change of the output state upon rotation. By rotating the circle using a rotator, the trajectories become a polarisation torus(S1×S1), which was experimentally confirmed in a simple setup using passive optical components together with the Mach–Zehnder interferometer. We also discuss the realisations of other topological features, such as a Möbius strip, a trefoil knot, Hopf links, and topological Dirac bosons, with a bulk-edge correspondence.
Actin polymerization and depolymerization in developing vertebrates
Authors: Bai Yang , Zhao Feng , Wu Tingting , Chen Fangchun , Pang Xiaoxiao
Published: September 2023

Development is a complex process that occurs throughout the life cycle. F-actin, a major component of the cytoskeleton, is essential for the morphogenesis of tissues and organs during development. F-actin is formed by the polymerization of G-actin, and the dynamic balance of polymerization and depolymerization ensures proper cellular function. Disruption of this balance results in various abnormalities and defects or even embryonic lethality. Here, we reviewed recent findings on the structure of G-actin and F-actin and the polymerization of G-actin to F-actin. We also focused on the functions of actin isoforms and the underlying mechanisms of actin polymerization/depolymerization in cellular and organic morphogenesis during development. This information will extend our understanding of the role of actin polymerization in the physiologic or pathologic processes during development and may open new avenues for developing therapeutics for embryonic developmental abnormalities or tissue regeneration.
Study on the effect of magnesium on leaf metabolites, growth and quality of tea tree
Authors: Zhang Ying , Zhang Qi , Wang Yuhua , Lin Shaoxiong , Chen Meihui , Cheng Pengyuan , Du Mengru , Jia Xiaoli , Ye Jianghua , Wang Haibin
Published: September 2023

Magnesium (Mg) is one of the essential elements for the growth of tea trees. In this study, we investigated changes in metabolites, photosynthetic fluorescence parameters and quality indexes of tea leaves under different concentrations of magnesium treatment, and the results showed that there were no significant differences in the quantity and total content of metabolites in tea leaves under different Mg concentrations. The results of volcano map analysis showed that the content of 235 metabolites in tea leaves showed an increasing trend and the content of 243 metabolites showed a decreasing trend with the increase of Mg concentration. The results of the combined analysis of the OPLS-DA model and bubble map showed that 45 characteristic metabolites were screened at different concentrations of Mg. Among these, the content of 24 characteristic metabolites showed an increasing trend and 21 characteristic metabolites showed a decreasing trend with the increase of Mg concentrations. The results of KEEG pathway enrichment showed that 24 characteristic metabolites with a upward trend were significantly enriched in saccharides metabolism, nucleic acid metabolism and vitamin metabolism, while the 21 characteristic metabolites with a downward trend were enriched in the synthesis of plant secondary metabolites, phenylpropanoid biosynthesis, biosynthesis of terpenoids, synthesis and metabolism of alkaloids, and synthesis and metabolism of amino acids. It can be inferred that Mg regulation was beneficial to enhance the photosynthetic capacity of tea trees, improve the accumulation and metabolism of carbohydrate substances in tea trees, and thus promoted the growth of tea trees, but was not conducive to the synthesis of secondary metabolites and amino acids related to tea quality. The results of photosynthetic fluorescence parameters and quality indexes of the tea tree confirmed the conclusion predicted by metabolomics. This study provided a reference for regulating of the growth and quality of tea trees with Mg fertilizer in tea plantations.
Transcriptome and hormone metabolome reveal the mechanism of stem bending in water lily (Nymphaea tetragona) cut-flowers
Authors: Li Jie , Sheng Yuhui , Xu Huixian , Li Qinxue , Lin Xiuya , Zhou Yang , Zhao Ying , Song Xiqiang , Wang Jian
Published: September 2023

Water lilies are popular ornamental cut-flowers with significant economic and cultural value. However, stem bending affects the preservation of cut-flowers during their vase life. To gain further insights into the molecular mechanisms of stem bending, transcriptome profiling, hormone measurement, and morphological analysis were performed using the stems of the ‘Blue Bird’ water lily. Transcriptome analysis revealed that 607 differentially expressed genes (DEGs) were associated with the dorsal and ventral stems of the water lily, of which 247 were up-regulated and 360 were down-regulated. Significant differences in genes associated with plant hormones, calcium ions, glucose metabolism, and photosynthesis pathways genes involved in the dorsal and ventral areas of the curved stem. In particular, DEGs were associated with the hormone synthesis, gravity response, starch granules, Ca2+ ions, and photosynthesis. The results of qRT-PCR were consistent with that of the transcriptome sequence analysis. A total of 12 hormones were detected, of which abscisic acid, indole-3-carboxaldehyde, indole-3-carboxaldehyde and jasmonic acid were significantly differentially expressed in the dorsal and ventral stems, and were significantly higher in the dorsal stem than in the ventral stem. The cell morphology in the dorsal and ventral areas of the curved stem clearly changed during vase life. The direction of starch granule settlement was consistent with the bending direction of the water lily stem, as well as the direction of gravity. In conclusion, stem bending in water lily cut-flowers is regulated by multiple factors and genes. This study provides an important theoretical basis for understanding the complex regulatory mechanism of water lily stem bending.
Genome-wide characterization of the soybean DOMAIN OF UNKNOWN FUNCTION 679 membrane protein gene family highlights their potential involvement in growth and stress response
Authors: Nawade Bhagwat , Bosamia Tejas C. , Lee Jae Hyun , Jang Jin Hoon , Lee Ok Ran
Published: September 2023

The DMP (DUF679 membrane proteins) family is a plant-specific gene family that encodes membrane proteins. The DMP family genes are suggested to be involved in various programmed cell death processes and gamete fusion during double fertilization in Arabidopsis. However, their functional relevance in other crops remains unknown. This study identified 14 genes from the DMP family in soybean (Glycine max) and characterized their physiochemical properties, subcellular location, gene structure, and promoter regions using bioinformatics tools. Additionally, their tissue-specific and stress-responsive expressions were analyzed using publicly available transcriptome data. Phylogenetic analysis of 198 DMPs from monocots and dicots revealed six clades, with clade-I encoding senescence-related AtDMP1/2 orthologues and clade-II including pollen-specific AtDMP8/9 orthologues. The largest clade, clade-III, predominantly included monocot DMPs, while monocot- and dicot-specific DMPs were assembled in clade-IV and clade-VI, respectively. Evolutionary analysis suggests that soybean GmDMPs underwent purifying selection during evolution. Using 68 transcriptome datasets, expression profiling revealed expression in diverse tissues and distinct responses to abiotic and biotic stresses. The genes Glyma.09G237500 and Glyma.18G098300 showed pistil-abundant expression by qPCR, suggesting they could be potential targets for female organ-mediated haploid induction. Furthermore, cis-acting regulatory elements primarily related to stress-, hormone-, and light-induced pathways regulate GmDMPs, which is consistent with their divergent expression and suggests involvement in growth and stress responses. Overall, our study provides a comprehensive report on the soybean GmDMP family and a framework for further biological functional analysis of DMP genes in soybean or other crops.
Preharvest and postharvest techniques that optimize the shelf life of fresh basil (Ocimum basilicum L.): a review
Authors: Brindisi Lara J. , Simon James E.
Published: September 2023

Basil (Ocimum basilicum L.) is a popular specialty crop known for its use as a culinary herb and medicinal plant around the world. However, its profitability and availability are limited by a short postharvest shelf life due to poor handling, cold sensitivity and microbial contamination. Here, we comprehensively review the research on pre- and postharvest techniques that extend the shelf life of basil to serve as a practical tool for growers, distributors, retailers and scientists. Modifications to postharvest storage conditions, pre- and postharvest treatments, harvest time and preharvest production methods have been found to directly impact the quality of basil and its shelf life. The most effective strategies for extending the shelf life and improving the quality of basil are discussed and promising strategies that research and industry employ are identified.
Silage preparation and sustainable livestock production of natural woody plant
Authors: Du Zhumei , Yang Fuyu , Fang Jiachen , Yamasaki Seishi , Oya Tetsuji , Nguluve Damiao , Kumagai Hajime , Cai Yimin
Published: September 2023

As the global population increases and the economy grows rapidly, the demand for livestock products such as meat, egg and milk continue to increase. The shortage of feed in livestock production is a worldwide problem restricting the development of the animal industry. Natural woody plants are widely distributed and have a huge biomass yield. The fresh leaves and branches of some woody plants are rich in nutrients such as proteins, amino acids, vitamins and minerals and can be used to produce storage feed such as silage for livestock. Therefore, the development and utilization of natural woody plants for clean fermented feed is important for the sustainable production of livestock product. This paper presents a comprehensive review of the research progress, current status and development prospects of forageable natural woody plant feed resources. The nutritional composition and uses of natural woody plants, the main factors affecting the fermentation of woody plant silage and the interaction mechanism between microbial co-occurrence network and secondary metabolite are reviewed. Various preparation technologies for clean fermentation of woody plant silage were summarized comprehensively, which provided a sustainable production mode for improving the production efficiency of livestock and producing high-quality livestock product. Therefore, woody plants play an increasingly important role as a potential natural feed resource in alleviating feed shortage and promoting sustainable development of livestock product.
Physiological cold tolerance evolves faster than climatic niches in plants
Authors: Wen Yin , Ye Qing , Román-Palacios Cristian , Liu Hui , Wu Guilin
Published: September 2023

Understanding how plants respond to thermal stress is central to predicting plant responses and community dynamics in natural ecosystems under projected scenarios of climate change. Although physiological tolerance is suggested to evolve slower than climatic niches, this comparison remains to be addressed in plants using a phylogenetic comparative approach. In this study, we compared i) the evolutionary rates of physiological tolerance to extreme temperatures with ii) the corresponding rates of climatic niche across three major vascular plant groups. We further accounted for the potential effects of hardening when examining the association between physiological and climatic niche rates. We found that physiological cold tolerance evolves faster than heat tolerance in all three groups. The coldest climatic-niche temperatures evolve faster than the warmest climatic-niche temperatures. Importantly, evolutionary rates of physiological cold tolerance were faster than rates of change in climatic niches. However, an inverse association between physiological cold tolerance and responding climatic niche for plants without hardening was detected. Our results indicated that plants may be sensitive to changes in warmer temperatures due to the slower evolutionary rates of heat tolerance. This pattern has deep implications for the framework that is being used to estimate climate-related extinctions over the upcoming century.
Efficient Agrobacterium-mediated transformation and genome editing of Fagopyrum tataricum
Authors: Pinski Artur , Betekhtin Alexander
Published: September 2023

Fagopyrum tataricum (L.) Gaertn. is an exceptional crop known for its remarkable health benefits, high levels of beneficial polyphenols and gluten-free properties, making it highly sought-after as a functional food. Its self-fertilisation capability and adaptability to challenging environments further contribute to its potential as a sustainable agricultural option. To harness its unique traits, genetic transformation in F. tataricum is crucial. In this study, we optimised the Agrobacterium-mediated transformation protocol for F. tataricum callus, resulting in a transformation rate of regenerated plants of approximately 20%. The protocol’s effectiveness was confirmed through successful GUS staining, GFP expression, and the generation of albino plants via FtPDS gene inactivation. These results validate the feasibility of genetic manipulation and highlight the potential for trait enhancement in F. tataricum.
Electrophysiological correlates of semantic pain processing in the affective priming
Authors: Gilioli Anna , Borelli Eleonora , Serafini Luana , Pesciarelli Francesca
Published: September 2023

Introduction

Pain plays a fundamental role in the well-being of the individual, and its semantic content may have specific properties compared to other negative domains (i.e., fear and anger) which allows the cognitive system to detect it with priority. Considering the influence of the affective context in which stimuli (targets) are evaluated, it is possible that their valence could be differentially processed if preceded by negative stimuli (primes) associated with pain than negative stimuli not associated with pain. Thus, the present study aims to investigate the electrophysiological correlates of the implicit processing of words with pain content by using an affective priming paradigm.

Methods

Event-related potentials (ERPs) were recorded while participants were presented with positive and negative word targets (not associated with pain) that were preceded by positive, negative (not associated with pain), and pain word primes. Participants were asked to judge the valence of the target word.

Results

Results showed faster reaction times (RTs) in congruent conditions, especially when the negative target was preceded by a pain prime rather than a positive one. ERPs analyses showed no effect of pain at an early-stage processing (N400), but a larger waveform when the pain prime preceded the positive prime on the LPP.

Discussion

These results reaffirm the importance that valence has in establishing the priority with which stimuli are encoded in the environment and highlight the role that pain has in the processing of stimuli, supporting the hypothesis according to which the valence and the semantics of a stimulus interact with each other generating a specific response for each type of emotion.
Perspectives of patients with advanced or metastatic non-small cell lung cancer on symptoms, impacts on daily activities, and thresholds for meaningful change: a qualitative research study
Authors: Cardellino Anna , Shah Manasee , Hanlon Jennifer , Kelly Kimberly , Martin Alexandra , Roborel de Climens Aude , Taiyari Sara , Stojadinovic Alexander
Published: September 2023

Introduction

Advanced or metastatic non-small cell lung cancer (NSCLC) is associated with significant symptom burden. It is important to understand the impact of these disease-and treatment-related symptoms on patients’ daily lives and explore from a patient perspective what constitutes a meaningful change in NSCLC symptoms.

Methods

Patient experience of advanced or metastatic NSCLC was explored in this prospective, non-interventional qualitative research study recruiting patients from the United States (US). Interviews were conducted to explore the most important symptoms, daily life impacts, and patients’ perspectives of what constitutes meaningful change when considering their current symptoms versus 6–12 months prior, based on the Patient Global Impression of Severity (PGI-S) and Patient Global Impression of Change (PGI-C) items.

Results

Between February and April 2022, 19 US-based patients with Stage IV NSCLC were recruited; 95% were female, 63% were White, 79% had been diagnosed >1 year prior, and 63% were receiving targeted therapy. Over half the patients indicated their most important symptoms were fatigue, shortness of breath, and cough. Patient differentiation between whether symptoms were disease- or treatment-related lacked concordance, and often patients were unable to distinguish the two. The most frequently mentioned impacts of these symptoms on patients’ daily lives were difficulty walking, sleep disturbance, anxiety/depression, impact on relationships, and difficulty doing daily tasks. Most patients considered a one-point change on the PGI-S or PGI-C to be meaningful based on rating their symptom severity at the time of the interview compared with 6–12 months before the interview.

Conclusion

Based on their own symptom experience, patients with advanced or metastatic NSCLC indicated a one-point threshold for meaningful change, whether improvement or worsening. This suggests a one-point change on the PGI-S or PGI-C may be a potential anchor for patient-reported outcome (PRO) endpoints used in clinical trials. It is important to use PRO instruments that capture the symptoms and impacts identified as most important to patients. These findings highlight the importance of using qualitative methods to assess disease-related symptoms, treatment-related side effects, and the impacts on daily life for patients with advanced or metastatic NSCLC, underscoring how qualitative assessments can complement quantitative PRO instruments for evaluating clinical trials.
Place and place names: a unified model
Authors: Ursini Francesco-Alessio , Zhang Yue Sara
Published: September 2023

The goal of this paper is to offer a unified account of Place as a central theoretical notion across different disciplines. We show that while psychology, geography and other sciences have been converging to a unified view of this notion, linguistics still offers a fragmented perspective. Consequently, place names lack a full-fledged analysis that connects this category to the psychological concept of place. We propose to overcome thisimpasseby introducing a multi-modal Discourse Representation Theory (DRT) account of place as a conceptual construct and place concepts as specific instances of this construct. We show that current variants of DRT permit us to model place names and their senses, i.e., the meaning(s) that individuals associate withSydney. We then model non-linguistic place concepts, i.e., the mental representation(s) that individuals can have of the city carrying this name. We present a model of the relation between linguistic meaning and conceptual content via the notion of anchoring relations applied to place. We pair this formal treatment with a morpho-syntactic account of place names building on current generative syntax treatments of proper names. Once we have a morpho-syntactic and semantic model of place names, we use a frame semantics treatment to account for lexical relations among place names. We test the overarching model on a set of recalcitrant problems afflicting current linguistic and multi-disciplinary treatments of place. These are the grammatical complexity and lexical content of place names, place concepts and their networks, and inter-subjective, communicative models of place in discourse. By solving these problems, our account integrates several frameworks (DRT, conceptual analysis, generative syntax, frame semantics) and connects several disciplines (linguistics, psychology, geographic information science, communication models) via a novel, multi-modal account of place. We conclude by discussing the theoretical and empirical import of these results.
The relationship between personality traits and willingness to undergo cosmetic surgery in the non-clinical population – a systematic review and meta-analysis
Authors: Lăzărescu Gianina-Mălina , Vintilă Mona
Published: September 2023

Objective

Conducting a systematic review and meta-analysis to synthesize previously obtained results regarding the relationship between interest in cosmetic surgery and personality traits.

Methodology

A series of criteria were applied (at the level of design, independent variables, dependent variable, participants) in order to decide which existing studies could be considered eligible for inclusion in the meta-analytic procedure. The identification of research that met the eligibility criteria was carried out with the help of the electronic search function in the following databases: ScienceDirect, PsycInfo, Web of Science, Scopus, Springer, and PubMed. Following this approach left 13 studies that were then subjected to the final analysis and included in the meta-analysis.

Results

The researchers’ expectations were partially supported by the results of the analyses, thus demonstrating the existence of a significant relationship between perfectionism (socially prescribed perfectionism; perfectionistic self-promotion), appearance-based rejection sensitivity, and interest in pursuing esthetic surgery.

Discussions

Identifying these relationships will allow cosmetic surgeons to understand both the mechanisms underlying this decision and the need for psychological assessment/counseling before patients undergo such procedures. It will also allow psychologists to develop best practice guidelines for how they relate to the patient before they perform cosmetic surgery. At the same time, psychotherapists will be able to devise targeted and personalized interventions for each personality profile, so that the decision to undergo an esthetic operation is not made based on a dispositional trait (fear of rejection, stress caused by body dissatisfaction).
Perspective on clinical high-risk for psychosis in Africa
Authors: Awhangansi Sewanu , Okewole Adeniran , Archard Philip John , O’Reilly Michelle
Published: September 2023

Clinical High Risk for Psychosis has evolved in recent years as a conceptual and clinical entity, representing a shift in focus from the syndromal psychosis state to a recognition of the pre-psychotic state as a period of potential preventive intervention. Much existing evidence has been generated from well-resourced countries, with a more limited body of literature available from Africa and other Majority World countries. Against a backdrop of prevailing systemic challenges, it is necessary to appraise the state of knowledge on Clinical High Risk for Psychosis in Africa. In this perspective article, we cover epidemiology, risk factors, predictors of psychosis conversion, as well as an overview of sociocultural factors, notably stigma, and the barriers to mental health services in African settings. We discuss existing and promising assessment approaches and reflect on preventive and early intervention strategies. We conclude with recommendations including the need for more clinical, longitudinal, and collaborative research anchored in an integrative transdisciplinary approach. We highlight the need for more culturally valid assessment tools and strategies to improve access to and utilization of services while also reducing stigma.
Factors associated with health behaviors in preventing non-communicable diseases among older adults living alone in poverty in Japan
Authors: Imamatsu Yuki , Tadaka Etsuko
Published: September 2023

Introduction

Older adults who live alone in poverty are highly susceptible to non-communicable diseases and other adverse conditions owing to health disparities resulting from social structures. However, the factors associated with health behavior to prevent non-communicable diseases in this population are rarely explored. The purpose of this study was to identify factors associated with health behavior to prevent non-communicable diseases among older adults living alone in poverty.

Methods

We conducted a self-administered mail survey covering 2,818 older adults living alone who were receiving public assistance, randomly selected from lists of individuals receiving national public assistance in all 1,250 local social welfare offices across Japan. A total of 1,608 individuals completed the questionnaire, a valid response rate of 57.1%. Respondents’ mean age was 74.5 years (standard deviation = 6.7), and 52.9% were women. The study variables included demographic characteristics, scores on a health behavior scale for older adults living alone and receiving public assistance (HBSO), and individual and community-related factors.

Results

Logistic regression analysis revealed that the individual factor of having a health check-up in the past 12 months [odds ratio (OR): 1.45, 95% confidence interval (CI): 1.10–1.91] and the community-related factors Lubben social network scale score (OR 1.15, 95% CI: 1.12–1.18) and Community Commitment Scale score (OR: 1.04, 95% CI: 1.00–1.08) were significantly associated with HBSO scores.

Conclusion

To improve health behavior among older adults living alone in poverty in Japan, social structures, such as lowering mental barriers to the detection, treatment, and management of non-communicable diseases and developing human resources, should be changed to provide social support, such that these individuals are not only dependent on family and friends.