bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains
Authors: Renner Susanne S , Scherz Mark D , Schoch Conrad L , Gottschling Marc , Vences Miguel
Published: November 2023

Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curating sequences derived from nomenclatural type material, which is the only way to improve the quality of DNA-based identification in the long run. For prokaryotes, 18,281 genome assemblies from type strains have been curated by NCBI staff and improve the quality of prokaryote naming. For Fungi, type-derived sequences representing over 21,000 species are now essential for fungus naming and identification. For the remaining eukaryotes, however, the numbers of sequences identifiable as type-derived are minuscule, representing only 739 species of arthropods, 1542 vertebrates, and 125 embryophytes. An increase in the production and curation of such sequences will come from (i) sequencing of types or topotypic specimens in museum collections, (ii) the March 2023 rule changes at the International Nucleotide Sequence Database Collaboration requiring more metadata for specimens, and (iii) efforts by data submitters to facilitate curation, including informing NCBI curators about a specimen’s type status. We illustrate different type-data submission journeys and provide best-practice examples from a range of organisms. Expanding the number of type-derived sequences in DNA databases, especially of eukaryotes, is crucial for capturing, documenting, and protecting biodiversity.
Social Protection and Foundational Cognitive Skills during Adolescence: Evidence from a Large Public Works Program
Authors: Freund Richard , Favara Marta , Porter Catherine , Behrman Jere
Published: November 2023

Many low- and middle-income countries have introduced public works programs (PWPs) to fight poverty. This paper provides the first evidence that children from families who benefit from PWPs show increased foundational cognitive skills. The results, based on unique tablet-based data collected as part of a long-standing longitudinal survey, show positive associations between participation in the Productive Safety Net Programme (PSNP) in Ethiopia during childhood with long-term memory and implicit learning, and suggestive evidence for working memory. These associations appear to be strongest for children whose households were still PSNP participants in the year of data collection. Evidence suggests that the association with implicit learning may be operating partially through children's time reallocation away from unpaid labor responsibilities, while the association with long-term memory may in part be due to the program's success in remediating nutritional deficits caused by early-life rainfall shocks.
High Diversity ofEpicoccumSpecies Associated with Leaf Spot on Italian Ryegrass in Southwestern China: Six New Records and Three New Species
Authors: Xu Zhiting , Xu Lingling , Liu Jiaqi , Chen Dongying , Cui Huawei , Xue Longhai , Li Chunjie
Published: November 2023

Italian ryegrass is widely cultivated for the production of forage, hay, and silage because of its high nutritional value and good palatability. Leaf spots caused by fungi pose a serious threat to forage crops. In order to expand the knowledge of fungi causing leaf spots in ryegrass (Lolium multiflorum) in Sichuan, Yunnan, Chongqing, and Guizhou of southwestern China, a comprehensive survey was undertaken from 2015 to 2022. The survey discovered that Epicoccum leaf spot (ELS) was a common and widespread disease, more serious at the late stage of growth (after late May). Symptomatic leaf samples collected from the four different provinces were analyzed, and a total of 202 Epicoccum isolates were obtained. Based on both multilocus phylogeny (ITS, LSU, TUB2, and RPB2) and morphology, 10 Epicoccum species were finally identified, including three novel species (E. endololii sp. nov., E. lolii sp. nov., and E. loliicola sp. nov.), six new host records (E. draconis, E. endophyticum, E. oryzae, E. plurivorum, E. thailandicum, and E. tobaicum), and an unknown species (Epicoccum sp.1). Pathogenicity tests showed that E. endophyticum, E. endololii, and Epicoccum sp.1 were nonpathogenic to Italian ryegrass, which were confirmed as endophytes in this study; the other six species could infect Italian ryegrass and cause leaf lesions to different degrees, of which E. draconis was more aggressive (P ≤ 0.05). Coupled with the isolation rates and geographical distributions of these species, it was found that E. plurivorum was the predominant pathogen in Yunnan while E. oryzae and E. tobaicum were the predominant pathogens in the other three provinces. This work provides an initial understanding of the taxonomy, virulence, and distribution of Epicoccum species associated with ELS in southwestern China and lays a solid foundation for the diagnosis in the field and scientific control of ELS on Italian ryegrass.
Three Decades of Rust Surveys in the United States Reveal Drastic Virulence Changes in Oat Crown Rust
Authors: Moreau Erin L. P. , Riddle Jakob M. , Nazareno Eric S. , Kianian Shahryar F.
Published: November 2023

To better understand how the pathogenicity of the oat crown rust pathogen Puccinia coronata f. sp. avenae (Pca) has changed in the United States, 30 years of United States Department of Agriculture (USDA) survey isolates (n = 5,456) tested on 30 to 40 differential lines were analyzed for overall and Pc-resistance-gene-specific virulence trends and correlations. Pca is incredibly pathologically diverse, with 88% of races represented by a single isolate. There are a slightly higher proportion of unique races from the Northern region of the United States, and for one fourth of the years, Northern region isolates were significantly more virulent than Southern isolates, which supports the idea that sexual recombination in this region is mediated by the alternate host as a major factor in creating new races. However, there is also support for regular isolate movement between North and South regions as isolates in the United States are steadily accumulating virulences at a rate of 0.35 virulences per year. Virulence significantly increased for 23 and decreased for four of the 40 differential lines. In the past few years, virulence has reached 90% or greater for 16 differential lines. There were also strong correlations in virulence for certain Pc genes that are likely identical, allelic, or target the same or closely linked pathogen effectors (e.g., Pc39, Pc55, and Pc71), and the results were largely in concordance with recent genome-wide association study (GWAS) effector studies using USDA isolate subsets. Understanding changes in Pca pathogenicity is essential for the responsible deployment and management of Pc resistance genes for sustainable and profitable oat production.
Reconstruction of Complex Anterior Chest Wall Defects: The Lasagna Technique
Authors: Baccarani Alessio , Filosso Pierluigi , Marra Caterina , De Maria Federico , Blessent Claudio Gio Francesco , Ruggiero Ciro , Pappalardo Marco , Pedone Antonio , De Santis Giorgio
Published: November 2023

Background:

Sternal tumors are rare, comprising only 0.94% of all bone tumors, with the majority being sarcomas. An extensive composite defect is often the result of surgical resection. Reconstruction of this anatomical area is a challenge for plastic surgeons. Reconstruction must fulfil two different tasks: restoration of soft tissues and stabilization of the chest wall. Both are well defined, and many techniques have been historically proposed.

Methods:

We present the case of a 66-year-old man affected by sternal metastasis of lung non-small cell carcinoma with sarcomatoid features. After wide tumor resection, a large defect was created.

Results:

The patient underwent a complex multilayer reconstruction that combined multiple techniques: Gore DualMesh to reconstruct the pericardial plane and protect the heart muscle, omental flap to facilitate integration of the mesh, titanium bars to recreate chest wall stability, and bilateral pectoralis muscle flaps to cover hardware. This multilayer reconstruction was named the “lasagna technique.”

Conclusions:

Due to the rarity of primary malignancies of the sternum, it is difficult to standardize a therapeutic approach. For this reason, it is necessary to customize the surgical treatment by combining several techniques and materials. Our lasagna technique may be considered a valuable option in treating these complex reconstructive cases.
Hair Transplantation in the United States: A Population-based Survey of Female and Male Pattern Baldness
Authors: Knoedler Leonard , Ruppel Felix , Kauke-Navarro Martin , Obed Doha , Wu Mengfan , Prantl Lukas , Broer P. Niclas , Panayi Adriana C. , Knoedler Samuel
Published: November 2023

Background:

Androgenetic alopecia, the most common type of hair loss, can impair the patient’s overall mental health. Although there are pharmaceutical and surgical treatments available, little is known about the public standpoint toward hair transplantation (HT).

Methods:

A sample of individuals living in the United States (n = 1000; male and female participants were equally distributed) was asked to fill out the questionnaire. The online survey was conducted in June 2022.

Results:

Most participants (42%; n = 416) were between 41 and 60 years of age. Study participants frequently reported that, with their hair loss progressing, they would not feel attractive anymore (n = 400; 40%), nor as confident as before (n = 330; 33%). Although women with minimal hair loss were willing to spend a median price of $4000 [interquartile range (IQ) IQR $1000–$5000], women with extensive hair loss were willing to spend significantly more (median = $5000; IQR $3600–$6375; P = 0.011). This was reproducible in men (P = 0.033). Although significantly fewer women considered undergoing HT (430 women versus 447 men; P < 0.001), female participants were willing to pay more for their HT compared with men (P = 0.039).

Conclusions:

Individuals living in the United States consider hair loss to impair their attractiveness and regard HT as a valuable therapeutic option. More affordable and gender-specific HT should be subject to future research work.
Umbilical Complications That Require Surgical Intervention after Gynecologic Laparoscopic Surgery
Authors: Sano Risa , Oka Aiko , Hirata Eri , Ochiai Hiroko
Published: November 2023

Background:

In laparoscopic surgery, the trocar is often inserted through the umbilicus because of the ease of insertion and inconspicuous postoperative scar formation. However, postoperative complications that require plastic surgical intervention may occur to the umbilicus.

Methods:

We reviewed 14 patients who received plastic surgery for umbilical issues following gynecologic laparoscopic surgery in our department from January 2015 to September 2021.

Results:

Most complications requiring umbilical surgery post gynecologic laparoscopic surgery include local infections, scar contractures, ectopic endometriosis, and umbilical necrosis. Mass resection and umbilical formation procedures were performed under general or local anesthesia. After a follow-up period of 6 months following surgery, no incidences of tumor development or recurrence of infection were seen, and the hypertrophic scar at the wound site gradually healed after the complete removal of the tumor and adequate suturing. Pathologically, 90% of the cases with keloid-like collagen disorder had concomitant inflammatory diseases such as epidermal cysts and abscesses.

Conclusions:

The majority of umbilical complications associated with laparoscopic surgery were predicted to be due to implantation of epithelial and tumor components during laparoscopic surgery and delayed postoperative inflammation. Therefore, it is necessary to educate surgeons about general measures of local infection control and careful surgical manipulation to prevent umbilical problems associated with laparoscopic surgery.
Identifying the Best Reduction Point for Zygomatic Arch Fractures Using Surface Markers
Authors: Abdelazeem Mohamed H. , Nadershah Mohammed
Published: November 2023

This study aimed to describe a straightforward and efficient surgical technique for identifying the ideal point of reduction in isolated zygomatic arch fractures using preoperative radiopaque markers. In addition, a retrospective review of patient outcomes associated with this technique was conducted. The collected data encompassed demographics, injury side, mechanism of injury, time of injury, and classification of the isolated arch fracture. Measured outcomes included radiographic anatomic reduction, clinical facial symmetry, surgical operating time, and maximum interincisal mouth opening. Descriptive statistics were computed for each study variable. A total of 12 patients (10 males and 2 females) with an average age of 39.25 years (range: 26–60 y) were included in the study. The mechanisms of injury comprised road traffic accidents (6 patients, 50%), sports-related injuries (2 patients, 16.7%), occupational injuries (2 patients, 16.7%), and falls (2 patients, 16.7%). On average, patients presented 3 days after the injury (range: 1–14 d). The fracture classification according to Reyes and colleagues categorized 10 patients (83.3%) as type 4 and 2 patients (16.7%) as type 2. Coronoid impingement was observed in half of the patients (50%). The average surgical time was 15.4 minutes (range: 12–19 min). All patients exhibited optimal radiographic anatomic reduction, clinical facial symmetry, and maximum interincisal opening. In conclusion, this study demonstrates that the described technique is a simple and effective method for identifying the optimal reduction point in isolated zygomatic arch fractures.
Diagnosing and Managing Velopharyngeal Insufficiency in Patients With Cleft Palate After Primary Palatoplasty
Authors: Pitkanen Veera V. , Geneid Ahmed , Saarikko Anne M. , Hakli Sanna , Alaluusua Suvi A.
Published: November 2023

Velopharyngeal insufficiency (VPI) after palatoplasty is caused by improper anatomy preventing velopharyngeal closure and manifests as a hypernasal resonance, audible nasal emissions, weak pressure consonants, compensatory articulation, reduced speech loudness, and nostril or facial grimacing. A multidisciplinary team using multimodal instruments (speech analysis, nasoendoscopy, videofluoroscopy, nasometry, and magnetic resonance imaging) to evaluate velopharyngeal function should manage these patients. Careful monitoring of velopharyngeal function by a speech pathologist remains paramount for early identification of VPI and the perceptual assessment should follow a standardized protocol. The greatest methodology problem in CLP studies has been the use of highly variable speech samples making comparison of published results impossible. It is hoped that ongoing international collaborative efforts to standardize procedures for collection and analysis of perceptual data will help this issue. Speech therapy is the mainstay treatment for velopharyngeal mislearning and compensatory articulation, but it cannot improve hypernasality, nasal emissions, or weak pressure consonants, and surgery is the definitive treatment for VPI. Although many surgical methods are available, there is no conclusive data to guide procedure choice. The goal of this review article is to present a review of established diagnostic and management techniques of VPI.
Orbital Roof Decompression and Transposition of Orbital Contents for Treatment of Orbital Deviation Associated With Fibrous Dysplasia
Authors: Nuri Takashi , Kawabata Erina , Ueda Koichi
Published: November 2023

A 25-year-old male was admitted to our institute complaining of caudal deviation of orbit. Surgery was performed through a coronal incision, a subtarsal incision, and a lynch incision. The periosteum of the orbital roof was raised, and the supraorbital wall was shaved cephalad in reference to the nonaffected side. Then the periosteum was incised from the inferior margin of the orbit to the medial and lateral palpebral ligaments, and the periosteum of the orbital floor was raised until the inferior orbital fissure. After the circumferential intraorbital periosteal detachment, the orbital contents could be readily moved cephalad ward. The outer table of the calvarial bone was transplanted to the orbital floor, and the palpebral ligaments were fixed 5 mm cranially. In the 5-year follow-up, the patient’s visual function was normal, and no recurrence of fibrous dysplasia was observed.
A Patient With Lobular Capillary Hemangioma Originating From the Inferior Turbinate Following Cauterization With Silver Nitrate
Authors: Nakamura Masahiro , Anzai Takashi , Saeki Harumi , Ide Takuma , Inoshita Ayako , Takata Yusuke , Matsumoto Fumihiko
Published: November 2023

Lobular capillary hemangiomas (LCH), which usually originate in the skin and mucous membranes of the oral cavity, are uncommon from the posterior portion of the inferior turbinate. Although the exact cause of LCH in the nasal cavity has not been elucidated, trauma, caused by factors such as intranasal packing and habitual nose-picking, has been reported as one of the causes. In addition, 2 cases of LCH caused by submucosal resection with powered instrumentation to the inferior turbinate have been reported, suggesting that various types of traumas to the nasal mucosa can cause LCH. The authors report the first case of LCH formation in the posterior portion of the inferior turbinate after cauterization with silver nitrate.
Significant Reduction in Posttransplant Hepatocellular Carcinoma Recurrence in the Post 6-Mo Waiting Policy Era
Authors: Mahmud Nadim , Yagan Lina , Hoteit Maarouf A. , Reddy K. Rajender , Abt Peter L. , Abu-Gazala Samir
Published: November 2023

Background.

In 2015, the United Network for Organ Sharing implemented a policy introducing a 6-mo waiting period before granting model for end-stage liver disease exception points to liver transplant (LT) candidates with hepatocellular carcinoma (HCC). This study analyzes the policy impact on post-LT HCC recurrence.

Methods.

This was a United Network for Organ Sharing retrospective cohort study of patients with HCC who underwent LT from January 1, 2010, to May 31, 2019. HCC-specific data included alpha-fetoprotein, tumor characteristics, locoregional therapy (LRT), and explant data used to calculate the Risk Estimation of Tumor Recurrence After Transplant score. The primary exposure was pre–/post–policy era, divided on October 8, 2015. Survival analysis techniques were used to evaluate the unadjusted and sequentially adjusted association between policy era and HCC recurrence, accounting for competing risks.

Results.

A total of 7940 patients were included, 5879 (74.0%) pre–policy era and 2061 (26.0%) post–policy era. Post–policy patients were older, received more LRT, and had lower alpha-fetoprotein levels and smaller tumor sizes at transplant. Incidence rates of HCC recurrence were 19.8 and 13.7 events per 1000 person-years for pre– and post–policy eras, respectively. Post–policy era was associated with an unadjusted 35% reduction in the risk of HCC recurrence (P < 0.001). After adjusting for recipient, donor, and tumor characteristics at listing this association remained (subhazard ratio 0.69; 95% confidence interval, 0.55-0.86; P = 0.001); however, after additionally adjusting for LRT episodes and Risk Estimation of Tumor Recurrence After Transplant score, there was no longer a statistically significant association (subhazard ratio 0.77; 95% confidence interval, 0.59-1.00; P = 0.054).

Conclusions.

We observed a significant reduction in post-LT HCC recurrence after policy implementation. This may be due to waitlist selection of healthier patients, increased LRT utilization, and potential selection of favorable tumor biology.
How greedy is too greedy? A network toy model for evaluating the sustainability of biased evolutionary dynamics
Authors: Weinberger V. P. , Zalaquett N. , Abades S.
Published: November 2023

Modern humanity has changed the biosphere at a global scale, threatening its own sustainability. It is claimed that through technology humans maximize the extraction of energy from the natural system towards their own benefit, with rates of appropriation that surpass the time-scales for systemic adaptation. This time-decoupled coevolutionary dynamic is at the core of human societal unsustainability. Here, we developed
in silico
experiments of an open energy-based flowing network toy model of natural systems and study the effects that
greedy
evolutionary strategies, resembling human societal demands, have upon the performance and
scarcity tolerance
of the system. We aim to determine the flexibility that those biased evolutionary dynamics have for matching or surpassing natural evolution outcomes. We studied four different indexes of system’s growth and development (total system throughflow (TST), average mutual information, ascendency and entropy difference) and compare their scarcity tolerance and performance outcomes with respect to four different greedy scenarios. The results showed that greedy strategies rarely surpassed the tolerance and performance achieved by natural systemic evolution. The nature of the greedy scenarios developed were closely related to increases in TST and therefore, we emphasized this comparison. Here, the maximum percentage of greedy networks capable of surpassing natural dynamics was around one-third (approx.

35
%

). However, results suggest the existence of a space parameter where local increases of energy flow can outperform the outcomes of natural systemic evolution, but no evident network property seems to characterize those greedy networks. A mild inverse relationship was found between the number of links that greedy nodes have towards the output and their capacity to outpass the control evolution. As many of the human societal effect upon biospheric processes have dissipative byproducts, knowing that such dynamics might diminish the systems tolerance and performance suggest care in their (ab)use.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
Evolution of the polycrisis: Anthropocene traps that challenge global sustainability
Authors: Søgaard Jørgensen Peter , Jansen Raf E. V. , Avila Ortega Daniel I. , Wang-Erlandsson Lan , Donges Jonathan F. , Österblom Henrik , Olsson Per , Nyström Magnus , Lade Steven J. , Hahn Thomas , Folke Carl , Peterson Garry D. , Crépin Anne-Sophie
Published: November 2023

The Anthropocene is characterized by accelerating change and global challenges of increasing complexity. Inspired by what some have called a polycrisis, we explore whether the human trajectory of increasing complexity and influence on the Earth system could become a form of trap for humanity. Based on an adaptation of the evolutionary traps concept to a global human context, we present results from a participatory mapping. We identify 14 traps and categorize them as either global, technology or structural traps. An assessment reveals that 12 traps (86%) could be in an advanced phase of trapping with high risk of hard-to-reverse lock-ins and growing risks of negative impacts on human well-being. Ten traps (71%) currently see growing trends in their indicators. Revealing the systemic nature of the polycrisis, we assess that Anthropocene traps often interact reinforcingly (45% of pairwise interactions), and rarely in a dampening fashion (3%). We end by discussing capacities that will be important for navigating these systemic challenges in pursuit of global sustainability. Doing so, we introduce evolvability as a unifying concept for such research between the sustainability and evolutionary sciences.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
Green preferences sustain greenwashing: challenges in the cultural transition to a sustainable future
Authors: von Flüe Lukas , Efferson Charles , Vogt Sonja
Published: November 2023

Discussions of the environmental impact that revolve around monetary incentives and other easy-to-measure factors are important, but they neglect culture. Pro-environmental values will be crucial when facing sustainability challenges in the Anthropocene, and demand among green consumers is arguably critical to incentivise sustainable production. However, owing to asymmetric information, consumers might not know whether the premium they pay for green production is well-spent. Reliable monitoring of manufacturers is meant to solve this problem. To see how this might work, we develop and analyse a game theoretic model of a simple buyer–seller exchange with asymmetric information, and our analysis shows that greenwashing can exist exactly because reliable monitoring co-exists with unreliable monitoring. More broadly, promoting pro-environmental values among consumers might even amplify the problem at times because a manufacturer with significant market power can exploit both consumer preferences for sustainability and trustworthy monitoring to gouge prices and in extreme cases green wash in plain sight. We discuss several strategies to address this problem. Promoting accurate beliefs and a large-scale behavioural change based on pro-environmental values might be necessary for a rapid transition to a sustainable future, but recent evidence from the cultural evolution literature highlights many important challenges.

This article is part of the theme issue ‘Evolution and sustainability: gathering the strands for an Anthropocene synthesis’.
Evaluation of physicochemical and biological properties of python fat
(Python bivittatus)
Authors: Quyen Pham Thi , Quoc Le Pham Tan
Published: November 2023

The main aim of this study was to determine python fat’s several
physicochemical properties, including dimensions, color, structure, acid value
(AV), saponification value (SV), density, and recovery efficiency. The optimum
yield obtained was approximately 80.40% at 180°C for 60 min with
an AV of 0.3366 and SV of 179.56 mg KOH/g. Fatty acids, comprising oleic acid
(72.462%), palmitic acid (26.243%), linolenic acid
(0.835%), and myristic acid (0.459%), were identified using gas
chromatography-mass spectrometry (GC-MS). The python fat had a very weak
antioxidant capacity and almost no antibacterial ability with gram-positive
(Staphylococcus aureus - ATCC 25923 and Bacillus
cereus - ATCC 10876) and gram-negative (Escherichia
coli - ATCC 25922 and Salmonella enterica - ATCC
35664) bacteria (used the paper disc diffusion method for antibiotic
susceptibility testing). Moreover, python fat is considered to be very resistant
to high temperatures.
Red wine quality of new Korean grape cultivar,
Ageude
Authors: Choi Jeong-Sil , Park Seo-Jun , Hur Youn-Young , Lee Dong-Hoon , Kim Su-Jin , Im Dongjun
Published: November 2023

This study aimed to investigate the wine properties of new Korean grape cultivar
Ageude. To this end, wine was produced using five grape
cultivars including Campbell Early and Muscat Bailey
A, which are commonly used for winemaking in Korea and
Pinot Meunier and Gamay, which are
European wine grape cultivars. We conducted a comprehensive analysis of wine
quality properties, color, and phenolic compounds and compared the variations
observed among these cultivars. The pH and total acid contents were in the
ranges of 3.75-4.57 and 0.39-0.58%, respectively. Specifically, the total
acid content of Ageude was 0.47% which was not high,
when compared to those of other wines. However, the soluble solid content was
7.85 °Brix, which was higher than those of the other wines. In terms of
color, the redness, color intensity, and hue values were all considerably high.
Moreover, the total phenolic content and total anthocyanin content of
Ageude were notably higher than those of the other
cultivars. However, it is worth noting that proanthocyanidin was not detected.
Based on these findings, Ageude is an excellent cultivar for
producing red wine, owing to its high total anthocyanin content and redness due
to the absence of proanthocyanidin, it is more suitable for producing short-term
aging wine rather than long-term aging wine.
CLAIR: An integrated lipid database across multiple crop species
Authors: He Bing , Bu Mengjia , Lin Qiang , Fu Zhengwei , Xie Junhua , Fan Wei , Li Jianyang , Li Ruonan , Hua Wei , Liu Wanfei , Cui Peng
Published: November 2023

Oilseed crops, which are rich in plant lipids, provide essential fatty acids for human consumption and serve as major sources of biofuels and essential raw materials for the chemical industry. As a result of population growth and ecological changes, the demand for vegetable oil is increasingly outpacing supply. A comprehensive understanding of the genes involved in lipid metabolism in oilseed crops and the regulatory relationships among these genes is essential for improving oil content. However, current studies on lipid metabolism genes rely heavily on a decade-old database of genes involved in lipid metabolism inArabidopsis thaliana. To address this issue, we mined the literature, integrated data from various databases and studies, and aligned homologs of lipid metabolism genes from nine oilseed crops to construct a comprehensive set of lipid metabolism genes in plants. Using this approach, we identified 221 additional lipid metabolism genes. In addition, we created a user-friendly lipid database called CLAIR (Crop Lipid-Associated Information Resource) by integrating and mining multi-omics data from nine major oil crops. The database is available athttp://www.clipair.cn/. These resources should facilitate further research and exploration of lipid metabolism in oil crops, ultimately contributing to improved oil production.
COL: a pipeline for identifying putatively functional back-splicing
Authors: Li Zheng , Sarker Bandhan , Zhao Fengyu , Zhou Tianjiao , Zhang Jianzhi , Xu Chuan
Published: November 2023

Circular RNAs (circRNAs) are a class of generally non-coding RNAs produced by back- splicing. Although the vast majority of circRNAs are likely to be products of splicing error and thereby confer no benefits to organisms, a small number of circRNAs have been found to be functional. Identifying other functional circRNAs from the sea of mostly non-functional circRNAs is an important but difficult task. Because available experimental methods for this purpose are of low throughput or versality and existing computational methods have limited reliability or applicability, new methods are needed. We hypothesize that functional back- splicing events that generate functional circRNAs (i) exhibit substantially higher back-splicing rates than expected from the total splicing amounts, (ii) have conserved splicing motifs, and (iii) show unusually high back-splicing levels. We confirm these features in back-splicing shared among human, macaque, and mouse, which should enrich functional back-splicing. Integrating the three features, we design a computational pipeline named COL for identifying putatively functional back-splicing. Different from the methods that require multiple samples, COL can predict functional back-splicing using a single sample. Under the same data requirement, COL has a lower false positive rate than that of the commonly used method that is based on the back- splicing level alone. We conclude that COL is an efficient and versatile method for rapid identification of putatively functional back-splicing and circRNAs that can be experimentally validated. COL is available athttps://github.com/XuLabSJTU/COL.
Two wildSpinaciaspecies,S. turkestanicaandS. tetrandra, genomes reveal a sex chromosome turnover in the genus
Authors: She Hongbing , Liu Zhiyuan , Xu Zhaosheng , Zhang Helong , Wu Jian , Wang Xiaowu , Cheng Feng , Charlesworth Deborah , Qian Wei
Published: November 2023

Spinach (Spinacia oleracea) is a dioecious species (with male and female flowers on separate individuals). Spinach and its closest wild relative,S. turkestanica, has homomorphic sex chromosomes, but the more distant relativeS. tetrandrahas heteromorphic sex chromosomes. We report high-quality genome assemblies forS. turkestanicaandS. tetrandra. These diverged approximately 6.3 million years ago (Mya), whileS. turkestanicasplit fromS. oleraceamuch more recently, around 0.8 Mya, supporting previous suggestions thatS. turkestanicais the direct progenitor of cultivated spinach. Using a combination of genomic approaches, we identified a sex-linked region (SLR) of ∼133 Mb inS. tetrandra. In all three species, the SLRs are within a large pericentromeric region of chromosome 4. We describe evidence that, inS. tetrandra, this region has completely stopped recombining in male meiosis, creating a large Y-linked region (YLR) that has partially degenerated; loss of recombination appears to have evolved in two events that created two “evolutionary strata”, one of which and is highly rearranged, relative to the X. The SLRs ofS. turkestanicaandS. oleraceaare much smaller: both include only a 10 Mb Y-specific region which is not detected inS. tetrandra. This was duplicated into a 14 Mb inverted region, and is termed the Y-duplicated region, or “YDR”. These findings suggest that a turnover event created the YDR before these species diverged, replacing an extensive ancestral Y-linked region like theS. tetrandraYLR.
Multi-modal breath measurements for biomarker discovery
Authors: Tomezsko Phillip J. , Wynn Jordan , Ostrinskaya Alla , Hendricks Jessie , Vian Trina
Published: November 2023

Breath contains numerous classes of compounds and biomolecules that could potentially be used as biomarkers for infectious disease as well as a range of other respiratory conditions or states. A testbed for simultaneous, multi-modal measurements was developed. Seventeen healthy subjects provided breath samples at baseline repiratory rate for particle size, lipid composition and bacterial nucleic acid composition analysis. The majority of the particles the participants exhaled at baseline were smaller than 5 μm, consistent with previous literature. The exhaled breath particulate contained lipids found in lung surfactant, indicating origin in the lung. Although bacterial DNA was not significantly higher in the exhaled breath particulate than in the environmental background, the metagenome of the breath was distinct from the environment, oral cavity and nasal passages of the participants. The low abundance of the breath microbiome limited analysis. The multi-modal breath testbed has promise for discovery of breath biomarkers and as a reference for biomarkers of different classes that are currently being used.
Diagnosis in Bytes: Comparing the Diagnostic Accuracy of Google and ChatGPT 3.5 as Diagnostic Support Tools
Authors: Guimaraes Guilherme R , Silva Caroline Santos , Contreras Jean Carlos Z , Figueiredo Ricardo G ,   Uros - Grupo de Pesquisa, Tiraboschi Ricardo B , Gomes Cristiano M , de Bessa Jose
Published: November 2023

Objective

Adopting digital technologies as diagnostic support tools in medicine is unquestionable. However, the accuracy in suggesting diagnoses remains controversial and underexplored. We aimed to evaluate and compare the diagnostic accuracy of two primary and accessible internet search tools: Google and ChatGPT 3.5.

Method

We used 60 clinical cases related to urological pathologies to evaluate both platforms. These cases were divided into two groups: one with common conditions (constructed from the most frequent symptoms, following EAU and UpToDate guidelines) and another with rare disorders - based on case reports published between 2022 and 2023 in Urology Case Reports. Each case was inputted into Google Search and ChatGPT 3.5, and the results were categorized as "correct diagnosis," "likely differential diagnosis," or "incorrect diagnosis." A team of researchers evaluated the responses blindly and randomly.

Results

In typical cases, Google achieved 53.3% accuracy, offering a likely differential diagnosis in 23.3% and errors in the rest. ChatGPT 3.5 exhibited superior performance, with 86.6% accuracy, and suggested a reasonable differential diagnosis in 13.3%, without mistakes. In rare cases, Google did not provide correct diagnoses but offered a likely differential diagnosis in 20%. ChatGPT 3.5 achieved 16.6% accuracy, with 50% differential diagnoses.

Conclusion

ChatGPT 3.5 demonstrated higher diagnostic accuracy than Google in both contexts. The platform showed acceptable accuracy in common cases; however, limitations in rare cases remained evident.
Dopamine neurons encode a multidimensional probabilistic map of future reward
Authors: Sousa Margarida , Bujalski Pawel , Cruz Bruno F. , Louie Kenway , McNamee Daniel , Paton Joseph J.
Published: November 2023

Learning to predict rewards is a fundamental driver of adaptive behavior. Midbrain dopamine neurons (DANs) play a key role in such learning by signaling reward prediction errors (RPEs) that teach recipient circuits about expected rewards given current circumstances and actions. However, the algorithm that DANs are thought to provide a substrate for, temporal difference (TD) reinforcement learning (RL), learns the mean of temporally discounted expected future rewards, discarding useful information concerning experienced distributions of reward amounts and delays. Here we present time-magnitude RL (TMRL), a multidimensional variant of distributional reinforcement learning that learns the joint distribution of future rewards over time and magnitude using an efficient code that adapts to environmental statistics. In addition, we discovered signatures of TMRL-like computations in the activity of optogenetically identified DANs in mice during a classical conditioning task. Specifically, we found significant diversity in both temporal discounting and tuning for the magnitude of rewards across DANs, features that allow the computation of a two dimensional, probabilistic map of future rewards from just 450ms of neural activity recorded from a population of DANs in response to a reward-predictive cue. In addition, reward time predictions derived from this population code correlated with the timing of anticipatory behavior, suggesting the information is used to guide decisions regarding when to act. Finally, by simulating behavior in a foraging environment, we highlight benefits of access to a joint probability distribution of reward over time and magnitude in the face of dynamic reward landscapes and internal physiological need states. These findings demonstrate surprisingly rich probabilistic reward information that is learned and communicated to DANs, and suggest a simple, local-in-time extension of TD learning algorithms that explains how such information may be acquired and computed.
Navigating the Nexus of Food Insecurity, Anxiety, and Depression in the Face of Climate Change: A Longitudinal Study in Rural Kenya
Authors: Goodman Michael , Raimer-Goodman Lauren , McPherson Heidi , Sharma Shreela , Ramphul Ryan , Woldu Dawit , Mukiri Fridah
Published: November 2023

Objective

To investigate the temporal relationships between food insecurity, anxiety, and depression among adult participants in a community-based empowerment program in Meru County, Kenya.

Methods

A cross-lagged panel analysis was conducted using data from 362 adult participants in a community-based empowerment program in Meru County, Kenya. Participants completed self-report measures of food insecurity, anxiety, and depression at two-time points, 11 weeks apart.

Results

Food insecurity (T1) predicted subsequent anxiety and depression (T2), controlling for within-variable, within-time, and control-variable correlations. Village-level food insecurity (T1) was correlated with significantly higher anxiety (T2). Additionally, anxiety (T1) predicted higher subsequent food insecurity (T2).

Conclusion

Food insecurity and anxiety have a complex bidirectional relationship. Interventions that address food security, mental health, and the psychosocial factors that promote adaptation to food-insecure environments are essential for promoting the well-being of individuals and communities in the face of climate change.
“If only these conversations had happened in induction.” Influencing employee aspiration with action learning-led inductions in the Big Four
Authors: Callaghan Deborah , Collins Helen
Published: November 2023

Purpose

This paper explores employee experiences of induction in the Big Four accountancy firms to understand how induction influences new recruits' career aspirations.

Design/methodology/approach

Using Bourdieusian sociology, this article adopts an interpretivist multi-method approach through focus groups and semi-structured interviews with 28 newly appointed accounting professionals. The study defines newly appointed as those who have experienced induction within the last two years of their employment.

Findings

The study's findings challenge the authenticity of induction from a shared employee consensus. It cites contagious spin, regarding career progression opportunities espoused during induction, at odds with the reality of work, ultimately contributing towards unfulfilled employee aspiration. As current strategies suggest that the intersection between employee aspiration and employer provision in the accountancy profession, is too broad, this study argues for more collaborative inductions. In addition, it proposes that accountancy firms should re-evaluate their current strategies and co-construct more authentic inductions that benefit all stakeholders to develop a stronger psychological contract that positively influences employee aspiration.

Research limitations/implications

The paper posits action-learning as a solution to address employee aspiration in induction campaigns in the accountancy profession.

Practical implications

As aspiration is the genesis of motivation and engagement, this study’s findings suggest that the use of an action-learning ethos in induction activities may provide an opportunity to explore the complexities of employee socialisation and provide a voice to new recruits attempting to influence any tensions or disappointment that may arise, as unmet career aspirations emerge.

Originality/value

The paper posits action learning as a solution to address employee aspiration in induction campaigns in the accountancy profession.
Impacts of parents' and guardians' trust in confessional schools on students’ perceived performance and spirituality
Authors: d'Angelo Marcia Juliana , Café Marisa Veloso , Rocha Raysa Geaquinto
Published: November 2023

Purpose

This study analyzes the impacts of trust in the confessional institution of primary education on a students’ spirituality and performance and the moderating effect of the families' religion on the relationship between trust in the school and the student's spirituality as perceived by parents and guardians.

Design/methodology/approach

This study takes the form of a survey with 346 parents and guardians from a Brazilian Adventist education network. The authors used partial least squares structural equation modeling by SmarPLS 4 to analyze the data.

Findings

The results reveal that parents' and guardians' trust in the confessional institution of primary education positively influences their perception of students' spirituality, which, in turn, has a positive impact on their performance. In addition, the families’ religion does not strengthen the relationship between school trust and students’ spirituality. It does not matter to which religious group the family belongs – as their overall spiritual development that favors the students’ academic performance.

Originality/value

The research contributes to the literature on school management, individual spirituality and relationship marketing – particularly customer relationship management in schools, involving parents, guardians and students.
SMEs' regional diversification: dynamic patterns and home market institutional determinants
Authors: Bai Wensong , Hilmersson Mikael , Johanson Martin , Oliveira Luis
Published: November 2023

Purpose

The authors seek to advance the understanding of small- and medium-sized enterprise (SME) internationalization at the regional level and examine the role of home market institutions in this process.

Design/methodology/approach

The authors analyze hypotheses with data from SMEs in five country markets and from the Global Entrepreneurship Monitor. A cluster analysis establishes the regional diversification patterns (based on regional diversification scope, speed and rhythm) and a multinomial regression tests the effect of home market institutions on their adoption.

Findings

The results offer a refined picture of SME regional diversification by revealing three patterns: intra-regionally focused firms, late inter-region diversifiers and early inter-region diversifiers. They also suggest that the adoption of these patterns is determined by SMEs' home market institutions.

Originality/value

The authors develop a nuanced understanding of SME internationalization by building upon and expanding the regionalization rationale in the internationalization patterns literature. Additionally, the authors address the acknowledged, yet rarely investigated, country-level determinants of internationalization patterns.
SMEs growth and profitability, productivity and debt relationships
Authors: Serrasqueiro Zélia , Pinto Beatriz , Sardo Filipe
Published: November 2023

Purpose

This study aims to seek to analyse the relationships between profitability, productivity, external debt and growth in SMEs. The authors also analyse firm size and age as explicative variables of small and medium-sized enterprise (SME) growth.

Design/methodology/approach

In this paper the data were collected for 3309 SMEs for the period 2010–2019. The authors estimate the model using the system generalised method of moments dynamic estimator.

Findings

The results show that after a certain level of profitability, this determinant positively impacts SME growth. Productivity influences positively the firm growth. There is a positive effect of external debt on SME growth, which can be explained by the insufficiency of internally generated funds. The authors obtained a negative signal between size and firm growth, contradicting Gibrat's Law (1931). Moreover, the results suggest that SMEs grow less after a certain age, suggesting that small firms grow less after reaching the minimum scale of efficiency.

Practical implications

For SME owner-managers, this study enhances the importance of profitability and labour productivity for firm growth. For policymakers, the results suggest the need for favourable conditions for SMEs in accessing external finance.

Originality/value

Profitability negatively impacts on SME growth. However, the authors found that above a certain level of profitability, probably, as firms accumulate retained earnings, profitability has a positive effect on SME growth. Moreover, this study shows that labour productivity and debt positively impact on SME growth, evidencing the importance of the availability of financial resources to sustain the growth of these firms.