bluuebunny/crossref_metadata_2025 huggingface dataset:
De novo genome assembly of a Geomyid rodent, Botta’s pocket gopher (Thomomys bottae bottae)
Authors: Voss Erin R , Escalona Merly , Kozak Krzysztof M , Seligmann William , Fairbairn Colin W , Nguyen Oanh , Marimuthu Mohan P A , Conroy Chris J , Patton James L , Bowie Rauri C K , Nachman Michael W
Published: August 2024

Botta’s pocket gopher (Thomomys bottae) is a common and widespread subterranean rodent of the North American West. The species has been of great interest to evolutionary biologists due to the phenotypic diversity and unusual levels of variation in chromosome number and composition observed across its range. Here, we present a high-quality reference genome from a male T. b. bottae individual captured in the San Francisco Bay Area. The assembly is comprised of 2,792 scaffolds, with a scaffold N50 value of 23.6 Mb and a BUSCO completeness score of 91.0%. This genome helps fill a significant taxonomic sampling gap in rodent genome resources. With this reference genome, we envision new opportunities to investigate questions regarding the genomics of adaptation to the belowground niche. Further, we can begin to explore the impact of associated life history traits, such as limited dispersal and low population connectivity, on intraspecific genetic and phenotypic variation, genome evolution, speciation, and phylogenetic relationships across the Geomyoidea.
Genetic risk, health-associated lifestyle, and risk of early-onset total cancer and breast cancer
Authors: Zhang Yin , Lindström Sara , Kraft Peter , Liu Yuxi
Published: August 2024

Background

Early-onset cancer (diagnosed under age 50) generally manifests as an aggressive disease phenotype. The association between healthy lifestyle and early-onset cancer and whether it varies by common genetic variants remains unclear.

Methods

We analyzed a prospective cohort of 66 308 participants who were under age 50 and free of cancer at baseline in the UK Biobank. Using Cox regression, we estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for early-onset total and breast cancer based on sex-specific composite total cancer polygenic risk scores (PRSs), a breast cancer-specific PRS, and sex-specific health-associated lifestyle scores (HLSs).

Results

In multivariable-adjusted analyses with 2-year latency, higher genetic risk (highest vs lowest tertile of PRS) was associated with significantly increased risks of early-onset total cancer in females (HR, 95% CI = 1.83, 1.49 to 2.26) and males (2.03, 1.51 to 2.73) as well as early-onset breast cancer in females (3.06, 2.20 to 4.26). An unfavorable lifestyle (highest vs lowest category of HLS) was associated with higher risk of total cancer and breast cancer in females across genetic risk categories; the association with total cancer and breast cancer was stronger in the highest genetic risk category than the lowest: HRs (95% CIs) were 1.55 (1.12 to 2.14) and 1.69 (1.11 to 2.57) in the highest genetic risk category and 1.03 (0.64 to 1.67) and 0.81 (0.36 to 1.85) in the lowest.

Conclusions

Genetic and lifestyle factors were independently associated with early-onset total and breast cancer risk. Individuals with a high genetic risk may benefit more from adopting a healthy lifestyle in preventing early-onset cancer.
Gerotherapeutics: aging mechanism–based pharmaceutical and behavioral interventions to reduce cancer racial and ethnic disparities
Authors: Mandelblatt Jeanne S , Antoni Michael H , Bethea Traci N , Cole Steve , Hudson Barry I , Penedo Frank J , Ramirez Amelie G , Rebeck G William , Sarkar Swarnavo , Schwartz Ann G , Sloan Erica K , Zheng Yun-Ling , Carroll Judith E , Sedrak Mina S
Published: August 2024

The central premise of this article is that a portion of the established relationships between social determinants of health and racial and ethnic disparities in cancer morbidity and mortality is mediated through differences in rates of biological aging processes. We further posit that using knowledge about aging could enable discovery and testing of new mechanism-based pharmaceutical and behavioral interventions (“gerotherapeutics”) to differentially improve the health of cancer survivors from minority populations and reduce cancer disparities. These hypotheses are based on evidence that lifelong differences in adverse social determinants of health contribute to disparities in rates of biological aging (“social determinants of aging”), with individuals from minoritized groups experiencing accelerated aging (ie, a steeper slope or trajectory of biological aging over time relative to chronological age) more often than individuals from nonminoritized groups. Acceleration of biological aging can increase the risk, age of onset, aggressiveness, and stage of many adult cancers. There are also documented negative feedback loops whereby the cellular damage caused by cancer and its therapies act as drivers of additional biological aging. Together, these dynamic intersectional forces can contribute to differences in cancer outcomes between survivors from minoritized vs nonminoritized populations. We highlight key targetable biological aging mechanisms with potential applications to reducing cancer disparities and discuss methodological considerations for preclinical and clinical testing of the impact of gerotherapeutics on cancer outcomes in minoritized populations. Ultimately, the promise of reducing cancer disparities will require broad societal policy changes that address the structural causes of accelerated biological aging and ensure equitable access to all new cancer control paradigms.
Clinical significance and potential mechanism of AEBP1 in glioblastoma
Authors: Wang Chengcheng , Han Huan , Cheng Fang , Wang Hao , Wang Junlong , Lv Chong , Jiang Shibin , Peng Yan , Zhao Xiaoling
Published: August 2024

Glioblastomas (GBM), the most common primary brain tumor, lack accurate prognostic markers and have a poor prognosis. Our study was designed to identify effective biomarkers for GBM prognosis analysis and development of precise treatments. Differentially expressed genes (DEGs) between GBM patients and controls were analyzed from the Xena database and GEPIA. Based on the screened DEGs, univariate COX and LASSO regression analysis were performed to identify the most relevant genes associated with GBM prognosis. Genes highly expressed in GBM patients were selected to construct receiver operating characteristic analysis and enrichment analysis was constructed on groups of high and low expression of adipocyte enhancer-binding protein 1 (AEBP1). CIBERSORT, ssGSEA and ESTIMATE were used to perform immune infiltration analysis. About 3297 DEGs were identified using data from Xena database; 8 prognostic genes were identified. AEBP1, which plays a role in neuronal differentiation and development, was positively correlated in GBMs with immune infiltration; its high expression in cancer patients is associated with short overall survival and advanced tumor staging. This study suggests that AEBP1 could serve as a prognostic marker for GBMs and that patients with high expression may have a better response to immunotherapy.
Introduction
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This introductory chapter is a brief overview on the history and functions of the United Nations Convention on Contracts for the International Sale of Goods (CISG). It describes the Convention’s four main parts and also indicates two fundamental differences from the Hague Conventions: rules governing the formation of the contract and those governing substantive sales law are brought together in one Convention. This avoids repetition and overlaps and makes it easier to clarify questions of detail, such as the necessity for statements to reach the other party. The CISG is also a ‘self-executing’ Convention, whereas the Hague Conventions were each drawn up as an annex to an international treaty and had to be brought into force. This chapter also outlines conflicting interests, though it reveals that the CISG can as a whole be viewed as a success and forward-looking.
Definition of ‘writing’
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter concerns Article 13. Article 13 ensures the autonomous interpretation of the term ‘writing’. Therefore the Article applies to all situations in which a requirement of writing applies in connection with a contract covered by the Convention. Consequently a notice under Article 21(2) may be sent by telex or telegram. Both forms would usually also fulfil a writing requirement under Article 29(2) or any other stipulated writing requirement. Moreover, Article 13 also determines the meaning of writing in Articles 12, 96 of the Convention. Furthermore, this outdated provision constitutes the clumsy attempt of the Vienna Conference to adjust the Convention to (at that time) new forms of communication. A permanent function of the provision is only developable, if it provides material concerning the openness of the Convention toward technological development, especially within the scope of Article 7.
Introduction to Articles 14–24 CISG: General questions regarding the formation of the contract
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter covers Part II of the Sales Convention (Articles 14–24). These govern the formation of international sales contracts. Articles 14–24 lay down contract formation rules in accordance with ‘traditional theory’, using ‘offer’ and ‘acceptance’ as the elements through which agreement between the parties is reached. In relying on the traditional offer-acceptance mechanism, Articles 14–24 therefore employ legal tools that should be familiar to almost every lawyer. As far as Part II occasionally also uses innovative approaches, those are limited to certain details. Under the Sales Convention’s contract formation rules, the parties’ mere consent suffices to make their sales agreement binding. In contrast to some domestic laws, the conclusion of a CISG contract is neither subject to any form requirements (Article 11) nor does it presuppose any additional indicia of seriousness.
Acceptance and its effectiveness
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter takes a look at Article 18. Under the Sales Convention’s contract conclusion regime, sales contracts are generally formed through two corresponding party declarations, ‘offer’ and ‘acceptance’. Article 18 is the introductory provision on acceptances and addresses two important aspects of this essential building block for contract formations. In particular, Article 18 governs two separate, but related matters: indication of offeree’s assent to an offer and effectiveness of an acceptance. The Article furthermore provides an overview of three types of acceptance: expressly declared acceptance, which must reach the offeror; impliedly declared acceptance, the expression of which must reach the offeror; and implied acceptance, which becomes effective with the conduct expressing acceptance.
Handing over of documents by seller
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter focuses on Article 34 which tackles the responsibility of sellers in terms of handing over documents. It notes the requirements of time, place and form of handing over documents along with the consequences of the seller's breach of contract. Under the Convention, the seller is not required to deliver documents relating to the goods to the buyer. However, it will be an obligation if it pertains to the parties' contract. Depending on the forum State's rules on international civil procedure, the place where the documents must be handed over may impact jurisdiction. The chapter also tackles the burden of proof for non-conformity of documents.
Incoterms and the CISG
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter discusses the commercial importance of Incoterms and the CISG. Incoterms are the world’s predominant set of short-hand trade terms for the sale of goods such as bulk and container transport. The Incoterms attempt a universal interpretation of the most widely used trade terms for worldwide application. The chapter also covers the legal nature of Incoterms as standardized contract terms and CISG contracts. The Incoterms use four different categories of trade terms: E, F, C, and D type terms. From E to D types, the obligations and costs gradually increase on the seller. Questions of Incoterm’s validity fall outside the CISG and will be determined by the otherwise applicable law.
Buyer’s right to avoid contract
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter expounds on the buyer’s right to avoid a contract. Article 49 covers the preconditions for the buyer’s right to avoid the contract in the event of the seller’s breach of contract. Avoidance of the contract results in the extinction of both parties’ obligations and in restitution of whatever has already been paid or supplied under the contract. Moreover, time limits are intended to clarify the fate of the contract and the mutual obligations of the parties. Avoidance of the contract under Article 49 assumes the seller failed to perform their obligations and breached its subsequent contract. The chapter also notes the requirements of the declaration of avoidance of the contract.
General obligations of the buyer
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter focuses on the general obligations of the buyer: to pay the purchase price and to take delivery of the goods. It discusses the determination of the purchase price and the applicable currency. Then it tackles the means of payment: open account, cash payment, or credit transfer; acceptance of a draft; documentary collection and documentary credits. The chapter likewise covers the place and time of payment, the interest of the due purchase price, partial payments, and imputation of payments, among others. Furthermore, it zooms in on the buyer’s obligation to provide security if he or she fails to duly pay the purchase price. Aside from securing the payment by implementing a documentary credit arrangement, the buyer may be required to provide additional security, usually by getting his or her banks to issue a payment guarantee or a standby letter of credit. In discussing the buyer’s obligation to take delivery of the goods, the chapter looks at supplying parts of the material necessary for the manufacture or production of the goods, specifications of the goods, incoterms, and duty to cooperate and inform. Moreover, it lays down the seller’s remedies in case of breach of contract by the buyer.
Buyer’s obligation to comply with governmental and banking procedures
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter emphasizes that the buyer’s obligation to pay the price entails taking steps and complying with formalities as may be required under the contract and any laws and regulations to enable payment to be made. It tackles compliance with governmental procedures as well as with banking procedures. The chapter also looks at the seller’s remedies for breach of contract by the buyer, and the situations wherein buyers are exempted from liability. It concludes with a brief discussion on the burden of proof: the seller has the burden of proof that the buyer was under an obligation associated with the payment and that he, in fact, breached this obligation.
Place of payment
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter focuses on the place of payment. It sets out a three-tier approach: the parties may contractually provide for the applicable place of payment, either by express agreement or by implicit agreement; if the parties have neither expressly nor impliedly agreed on the place of payment, the buyer must pay the purchase price at the place where the handing over of the goods or documents against payment takes place; if neither the parties have agreed on a place of payment nor the payment takes place against handing over of the goods or documents, the buyer has to pay the purchase price at the seller’s place of business. The chapter tackles contracts involving the carriage of goods and contracts involving goods stored in a third-party warehouse. The discussion also covers the place of payment of sums other than the purchase price.
Seller’s right to specify features of goods
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter discusses the situation wherein the seller may make the specification of the goods. This happens if under the contract, the buyer is to specify the form, measurement, or other features of the goods and he or she fails to make such specification either on the date agreed upon or within a reasonable time after receipt of a request from the seller. In this case, the seller may—without prejudice to any other rights that he may have—make the specification in accordance with the requirements of the buyer that may be known to him or her. This chapter underscores that if the seller makes the specification, he or she must inform the buyer of the details thereof and must fix a reasonable time within which the buyer may make a different specification. If, after receipt of such a communication, the buyer fails to do so within the time so fixed, the specification made by the seller is binding. The chapter also tackles the possible restrictions on the seller’s specification. Furthermore, it looks at other remedies available to the seller.
Loss after risk has passed
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter underscores that loss of or damage to the goods after the risk has passed to the buyer does not discharge him or her from the obligation to pay the price, unless the loss or damage is due to an act or omission of the seller. The discussion emphasizes that Article 66 is not in and of itself operative but rather sets out the Convention’s concept of the passing of risk. The chapter also tackles the now prevailing view which includes governmental interferences in the Convention’s notion of risk. Furthermore, it looks at the scope of Article 66 in fine, as well as the dispute over the standard for the seller’s conduct when determining, whether there was an ‘act or omission of the seller’ making the passing of risk irrelevant under Article 66 in fine. The discussion likewise covers the restriction of claim for the purchase price.
Avoidance of instalment contracts
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter looks closely at Article 73, which provides for special rules of contract avoidance where the performance of an instalment contract is impaired. The provision states that a fundamental breach regarding one instalment entitles the creditor to avoid the contract with regard to that instalment. It also deals with the likeliness of a future breach in an instalment contract; if a breach of duty with regard to the current instalment indicates that future instalments might be impaired, the creditor may avoid the contract for the future. Next, it draws further consequences for the whole contract from the breach of a single delivery: the buyer who declares the contract avoided with regard to a single instalment may at the same time avoid the contract in relation to prior and/or future instalments, if, because of their interdependence, the fundamental breach of the single instalment affects also the other instalments or the contract as a whole.
Calculation of damages in general
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter discusses Article 74, which governs the scope of the buyer’s or seller’s claim to compensation for the breach of contractual obligations. It expresses that the damages for breach of contract by one party consist of a sum equal to the loss, including loss of profit, suffered by the other party as a consequence of the breach. The provision contains two essential principles: the principle of full compensation and limitation of liability by the foreseeability rule. In explaining the scope of application of Article 74, the chapter discusses the breach of contractual obligations, breach of non-actionable duties, death and personal injury, and persons entitled to damages and third-party losses. It also describes the form of compensation to be made. The chapter tackles the categories of loss, the loss of profit, and the calculation of loss, among other topics.
Seller’s obligation to preserve the goods
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter describes the obligation that Article 86 places on a buyer who has received the goods but does not wish to retain them. It analyzes how Article 86 corresponds to the seller’s obligation to preserve the goods under Article 85, wherein the buyer is obliged to preserve the goods. A right to reject the goods may arise from any rule providing that the buyer may return the goods to the seller. The chapter emphasizes, contrary to the view sometimes expressed, that it is not necessary for the seller to manifest one’s intention to reject the goods immediately upon their receipt. The existence of an obligation to preserve the goods cannot depend on whether or not the buyer has definitely decided to reject them.
Reservation regarding Part II or III
Authors: Schwenzer Ingeborg , Schroeter Ulrich G
Published: August 2024

This chapter investigates Article 92, which allows a Contracting State to declare that it will not be bound by either Part II or Part III of the Sales Convention. It details how Article 92 reservation was included in the Sales Convention as a compromise upon initiative of the Nordic (Scandinavian) States. For Denmark, Finland, Norway and Sweden, Article 92 reservations with regard to Part II were subsequently in effect from their ratifications until 2012–14. The chapter describes the reservation under Article 92 that ranks as the most far-reaching reservation authorized under the CISG. The use of Article 92 by a State does not mean that the Convention’s rules in the reserved Part can never apply in the reservation State or to buyers and sellers from this State as Article 1(1)(b) may still result in their applicability.
A Gödel-Dugundji-style theorem for the minimal structural logic
Authors: Pawlowski Pawel , Ferguson Thomas M , Gertler Ethan
Published: August 2024

This paper introduces a sequent calculus, $\textbf{M}_{\textbf{S}}$, the minimal structural logic, which includes all structural rules while excluding operational ones. Despite its limited calculus, $\textbf{M}_{\textbf{S}}$ unexpectedly shares a property with intuitionistic logic and modal logics between $\textsf{S1}$ and $\textsf{S5}$: it lacks sound and complete finitely-valued (deterministic) semantics. Mirroring Gödel’s and Dugundji’s findings, we demonstrate that $\textbf{M}_{\textbf{S}}$ does possess a natural finitely-valued non-deterministic semantics. In fact, we show that $\textbf{M}_{\textbf{S}}$ is sound and complete with respect to any semantics belonging to a natural class of maximally permissive non-deterministic matrices. We close by examining the case of subsystems of $\textbf{M}_{\textbf{S}}$, including the “structural kernels” of the strict-tolerant and tolerant-strict logics $\textbf{ST}$ and $\textbf{TS}$, and strengthen this result to also preclude finitely-valued deterministic semantics with respect to variable designated value frameworks.
Testing Outlier Detection Algorithms for Identifying Early Stage Solute Clusters in Atom Probe Tomography
Authors: Stroud Ryan S , Al-Saffar Ayham , Carter Megan , Moody Michael P , Pedrazzini Stella , Wenman Mark R
Published: August 2024

Atom probe tomography (APT) is commonly used to study solute clustering and precipitation in materials. However, standard techniques used to identify and characterize clusters within atom probe data, such as the density-based spatial clustering applications with noise (DBSCAN), often underperform with respect to small clusters. This is a limitation of density-based cluster identification algorithms, due to their dependence on the parameter Nmin, an arbitrary lower limit placed on detectable cluster sizes. Therefore, this article attempts to consider the characterization of clustering in atom probe data as an outlier detection problem of which k-nearest neighbors local outlier factor and learnable unified neighborhood-based anomaly ranking algorithms were tested against a simulated dataset and compared to the standard method. The decision score output of the algorithms was then auto thresholded by the Karcher mean to remove human bias. Each of the major models tested outperforms DBSCAN for cluster sizes of <25 atoms but underperforms for sizes >30 atoms using simulated data. However, the new combined k-nearest neighbors (k-NN) and DBSCAN method presented was able to perform well at all cluster sizes. The combined k-NN and seven methods are presented as a new approach to identifying clusters in APT.
Galaxy evolution in modified gravity simulations: using galaxy properties to constrain our gravitational model
Authors: Pallero Diego , Gómez Facundo A , Padilla Nelson D , Jaffé Y L , Baugh Carlton M , Li Baojiu , Hernández-Aguayo César , Arnold Christian
Published: August 2024

We present a quantitative analysis of the properties of galaxies and structures evolving in universes dominated by different modified gravitational models, including two variants of the f(R)-gravity (F) and two of the Dvali–Gabdadze–Poratti (N) braneworld model, which respectively feature the chameleon and Vainshtein screening mechanisms. Using the Simulation HYdrodynamics BeyONd Einstein (shybone) cosmological hydrodynamical full-physics simulations suite, we study the departures in the properties of galaxies residing in different environments with respect to the standard model (GR). Using two different criteria to compare, we find that structures formed within modified gravity tend to show a denser gas density profile than their GR counterparts. Within the different modified gravity models, N1 and F5 gravity models show greater departures from the standard model, with gas density profiles $\rho _{\rm IGM} \ge 30~{{\ \rm per\ cent}}$ denser in the outskirts for the N1 model, and in the inner parts for the F5 model. Additionally, we find that haloes evolving in MG universes show, in general, larger quenched fractions than GR, reaching up to 20 per cent larger quenching fractions in F5 regardless of the stellar mass of the galaxy. Concerning the other models, F6, N1, and N5 show slightly larger quenched fractions, but no strong differences can be found. These results directly impact the colour distribution of galaxies, making them in MG models redder and older than their GR counterparts. Like GR, once the environment starts to play a role, galaxies rapidly get quenched, and the differences between models vanish.
What does not kill Gaia makes her stronger: impacts of external perturbations on biosphere evolution
Authors: Arthur R , Nicholson A E , Mayne N J
Published: August 2024

Life on Earth has experienced numerous upheavals over its approximately 4 billion year history. In previous work, we have discussed how interruptions to stability lead, on average, to increases in habitability over time, a tendency we called entropic Gaia. Here, we continue this exploration, working with the Tangled Nature Model of co-evolution, to understand how the evolutionary history of life is shaped by periods of acute environmental stress. We find that while these periods of stress pose a risk of complete extinction, they also create opportunities for evolutionary exploration which would otherwise be impossible, leading to more populous and stable states among the survivors than in alternative histories without a stress period. We also study how the duration, repetition and number of refugia into which life escapes during the perturbation affects the final outcome. The model results are discussed in relation to both Earth history and the search for alien life.
PlantCircRNA: a comprehensive database for plant circular RNAs
Authors: He Shutian , Bing Jianhao , Zhong Yang , Zheng Xiaoyang , Zhou Ziyu , Wang Yifei , Hu Jiming , Sun Xiaoyong
Published: August 2024

Circular RNAs (circRNAs) represent recently discovered novel regulatory non-coding RNAs. While they are present in many eukaryotes, there has been limited research on plant circRNAs. We developed PlantCircRNA (https://plant.deepbiology.cn/PlantCircRNA/) to fill this gap. The two most important features of PlantCircRNA are (i) it incorporates circRNAs from 94 plant species based on 39 245 RNA-sequencing samples and (ii) it imports the original AtCircDB and CropCircDB databases. We manually curated all circRNAs from published articles, and imported them into the database. Furthermore, we added detailed information of tissue as well as abiotic stresses to the database. To help users understand these circRNAs, the database includes a detection score to measure their consistency and a naming system following the guidelines recently proposed for eukaryotes. Finally, we developed a comprehensive platform for users to visualize, analyze, and download data regarding specific circRNAs. This resource will serve as a home for plant circRNAs and provide the community with unprecedented insights into these mysterious molecule.
Mechanism of structure-specific DNA binding by the FANCM branchpoint translocase
Authors: Abbouche Lara , Murphy Vincent J , Gao Jixuan , van Twest Sylvie , Sobinoff Alexander P , Auweiler Karen M , Pickett Hilda A , Bythell-Douglas Rohan , Deans Andrew J
Published: August 2024

FANCM is a DNA repair protein that recognizes stalled replication forks, and recruits downstream repair factors. FANCM activity is also essential for the survival of cancer cells that utilize the Alternative Lengthening of Telomeres (ALT) mechanism. FANCM efficiently recognizes stalled replication forks in the genome or at telomeres through its strong affinity for branched DNA structures. In this study, we demonstrate that the N-terminal translocase domain drives this specific branched DNA recognition. The Hel2i subdomain within the translocase is crucial for effective substrate engagement and couples DNA binding to catalytic ATP-dependent branch migration. Removal of Hel2i or mutation of key DNA-binding residues within this domain diminished FANCM’s affinity for junction DNA and abolished branch migration activity. Importantly, these mutant FANCM variants failed to rescue the cell cycle arrest, telomere-associated replication stress, or lethality of ALT-positive cancer cells depleted of endogenous FANCM. Our results reveal the Hel2i domain is key for FANCM to properly engage DNA substrates, and therefore plays an essential role in its tumour-suppressive functions by restraining the hyperactivation of the ALT pathway.
The molecular mechanism for TERRA recruitment and annealing to telomeres
Authors: Wondimagegnhu Bersabel , Ma Wen , Paul Tapas , Liao Ting-Wei , Lee Chun Ying , Sanford Samantha , Opresko Patricia L , Myong Sua
Published: August 2024

Telomeric repeat containing RNA (TERRA) is a noncoding RNA that is transcribed from telomeres. Previous study showed that TERRA trans anneals by invading into the telomeric duplex to form an R-loop in mammalian cells. Here, we elucidate the molecular mechanism underlying TERRA recruitment and invasion into telomeres in the context of shelterin proteins, RAD51 and RNase H using single molecule (sm) assays. We demonstrate that TERRA trans annealing into telomeric DNA exhibits dynamic movement that is stabilized by TRF2. TERRA annealing to the telomeric duplex results in the formation of a stable triplex structure which differs from a conventional R-loop. We identified that the presence of a sub-telomeric DNA and a telomeric overhang in the form of a G-quadruplex significantly enhances TERRA annealing to telomeric duplex. We also demonstrate that RAD51-TERRA complex invades telomere duplex more efficiently than TERRA alone. Additionally, TRF2 increases TERRA affinity to telomeric duplex and protects it from RNase H digestion. In contrast, TRF1 represses TERRA annealing to telomeric duplex and fails to provide protection against RNase H digestion. Our findings provide an in-depth molecular mechanism underpinning TERRA recruitment and annealing to the telomere.
Impact of Diet Modifications on Body Weight, Body Composition, Treatment Outcomes, and Quality of Life During Primary Treatment for Breast Cancer: A Systematic Review
Authors: Chakos Kaitlin , Pezley Lacey , Bryner Alyssa , Czyzewski Ola , Corral Jennifer , Marquina Vanessa , Gadi Vijayakrishna , Ganschow Pamela , Tussing-Humphreys Lisa , Gabel Kelsey
Published: August 2024

Context

Breast cancer is a significant public health challenge, with 290 000 new cases annually and significant healthcare costs. Treatment advancements have led to improvements in survival, but common adverse effects include weight gain, fatigue, nausea, and taste changes, decreasing quality of life.

Objective

This review aims to assess the impact of diet and lifestyle interventions during primary treatment for breast cancer and their effects on body weight, body composition, treatment-related adverse outcomes, and patient-reported quality of life.

Data Sources and Data Extraction

A search of PubMed, CINAHL, and EMBASE conducted through May 10, 2023, identified 31 publications describing 27 interventions including diet or diet plus exercise. The Cochrane Risk of Bias tool assessed the quality of publications.

Data Analysis

The findings suggest that whole foods, aerobic and strength-training exercises, and intermittent fasting during treatment may improve body weight and composition, treatment-related outcomes, and quality of life. Limitations include variation in study duration, small sample sizes, and limited sociodemographic data.

Conclusion

Improvements seen with increased diet quality and reduced caloric intake, with or without exercise, challenge current standard-of-care recommendations during treatment for breast cancer. While there is a need for additional research, healthcare teams can confidently promote healthy diets and exercise during primary treatment for breast cancer to manage weight and improve treatment-related side effects and quality of life.

Systematic Review Registration

PROSPERO registration no. 42023425613.
Immigrant overeducation across two generations: the role of gender and part-time work
Authors: Pineda-Hernández Kevin , Rycx François , Volral Mélanie
Published: August 2024

Overeducation implies having a higher level of education than that required to perform a specific job. In this regard, a large body of literature shows that first-generation immigrants born in developing countries experience a higher likelihood of being overeducated than natives due in part to their foreign origin (i.e. immigrant overeducation). However, evidence is remarkably scarce regarding the overeducation of second-generation immigrants. Using a matched employer–employee database for Belgium over the period 1999–2016 and generalized ordered logit regressions, we contribute to the literature with one of the first studies on the intergenerational nexus between overeducation and origin among tertiary-educated workers. Our estimates suggest that immigrant overeducation disappears across two generations, except for workers from the Near and Middle East and the Maghreb. Moreover, we show that immigrant overeducation is a persistent intergenerational phenomenon among part-time workers. Our gender-interacted estimates confirm this conclusion for both male and female workers.
The effector SJP3 interferes with pistil development by sustaining SHORT VEGETATIVE PHASE 3 expression in jujube
Authors: Deng Mingsheng , Ma Fuli , Zhai Liping , Zhang Xinyue , Zhang Ning , Zheng Yunyan , Chen Wei , Zhou Wenmin , Pang Kaixue , Zhou Junyong , Sun Qibao , Sun Jun
Published: August 2024

Jujube witches’ broom (JWB) is a phytoplasma disease that causes severe damage to jujube (Ziziphus jujuba) crops worldwide. Diseased jujube plants show enhanced vegetative growth after floral reversion, including leafy flower structures (phyllody) and the fourth whorl converting into a vegetative shoot. In previous research, secreted JWB protein 3 (SJP3) was identified as an inducer of phyllody. However, the molecular mechanisms of SJP3-mediated pistil reversion remain unknown. Here, the effector SJP3 was found to interact with the MADS-box protein SHORT VEGETATIVE PHASE 3 (ZjSVP3). ZjSVP3 was expressed in young leaves and during the initial flower bud differentiation of healthy jujube-bearing shoots but was constitutively expressed in JWB phytoplasma-infected flowers until the later stage of floral development. The SJP3 effector showed the same expression pattern in the diseased buds and promoted ZjSVP3 accumulation in SJP3 transgenic jujube calli. The N-terminal domains of ZjSVP3 contributed to its escape from protein degradation in the presence of SJP3. Heterologous expression of ZjSVP3 in Nicotiana benthamiana produced typical pistil abnormalities, including trichome-enriched style and stemlike structures within the leaflike ovary, which were consistent with those in the mildly malformed lines overexpressing SJP3. Furthermore, ectopic expression of ZjSVP3 directly bound to the zinc finger protein 8 (ZjZFP8) and MADS-box gene SHATTERPROOF 1 (ZjSHP1) promoters to regulate their expression, resulting in abnormal pistil development. Overall, effector SJP3-mediated derepression of ZjSVP3 sustained its expression to interfere with pistil development, providing insight into the mechanisms of pistil reversion caused by JWB phytoplasma in specific perennial woody plant species.
Obesity and age are transmission risk factors for SARS-CoV-2 infection among exposed individuals
Authors: Matamalas Joan T , Chelvanambi Sarvesh , Decano Julius L , França Raony F , Halu Arda , Santinelli-Pestana Diego V , Aikawa Elena , Malhotra Rajeev , Aikawa Masanori
Published: August 2024

The coronavirus disease (COVID-19) pandemic has occurred in Massachusetts in multiple waves led by a series of emerging variants. While the evidence has linked obesity with severe symptoms of COVID-19, the effect of obesity on susceptibility to SARS-CoV-2 infection remains unclear. Identification of intrinsic factors, which increase the likelihood of exposed individuals succumbing to productive SARS-CoV-2 infection could help plan mitigation efforts to curb the illness. We aim to investigate whether obese individuals have a higher susceptibility to developing productive SARS-CoV-2 infection given comparable exposure to nonobese individuals. This case–control study leveraged data from the Mass General Brigham's (MGB) electronic medical records (EMR), containing 687,813 patients, to determine whether obesity at any age increases the proportion of infections. We used PCR results of 72,613 subjects who tested positive to SARS-CoV-2 or declared exposure to the virus independently of the result of the test. For this study, we defined susceptibility as the likelihood of testing positive upon suspected exposure. We demonstrate evidence that SARS-CoV-2 exposed obese individuals were more prone to become COVID positive than nonobese individuals [adjusted odds ratio = 1.34 (95% CI: 1.29–1.39)]. Temporal analysis showed significantly increased susceptibility in obese individuals across the duration of the pandemic in Massachusetts. Obese exposed individuals are at a higher risk of getting infected with SARS-CoV-2. This indicates that obesity is not only a risk factor for worsened outcomes but also increases the risk for infection upon exposure. Identifying such populations early will be crucial for curbing the spread of this infectious disease.
When reasons run out
Authors: Kay Jason
Published: August 2024

Subjectivists about practical normativity hold that an agent's favouring and disfavouring attitudes give rise to practical reasons. On this view, an agent's normative reason to choose vanilla over chocolate ice cream ultimately turns on facts about what appeals to her rather than facts about what her options are like attitude-independently. Objectivists—who ground reasons in the attitude-independent features of the things we aim at—owe us an explanation of why it is rational to choose what we favour, if not simply because favouring is a source of reasons. My aim in this paper is to supply such a story. The proposal is roughly that when an agent cannot base her choices on her judgements about what she has most reason to do, structural rationality extends to her a license to choose something simply because she favours it, without imbuing favouring with the authority of a normative reason.
Surviving and Resisting Retrenchment: US Resettlement Organizations’ Responses to Trump-era Anti-refugee Policy
Authors: Howsam Scholl Jess , Darrow Jessica H
Published: August 2024

Retrenchment and erosion of refugee protections have been on the rise in multiple contexts around the world. In the United States, the Trump Administration’s refugee policies threatened the very survival of domestic resettlement institutions. The administration reduced the number of refugees, cut funds, and sewed confusion. In the face of restrictionist policies, how did refugee advocates respond? Leveraging a case study of resettlement organisations’ responses to Trump-era anti-refugee policies, this article demonstrates that administrators not only adapted creatively to survive the barrage of attacks but also engaged in meaningful political contestation. In circumscribed moments, administrators defied theoretical expectations: they placed the collective above the individual and challenged exploitative dynamics fundamental to US refugee programmes. This article draws on critical theory to analyse administrative resistance, repositioning bureaucrats as advocates in the process. In doing so, the article makes three main contributions. First, it elucidates the unseen role of bureaucrats as agents of progressive institutional change. Next, it offers new analytic purchase into puzzling organisational behaviour by foregrounding social relations of power. Finally, the article provides tools and resources for resettlement organisations navigating retrenchment globally.
The yellowhorn MYB transcription factor MYB30 is required for wax accumulation and drought tolerance
Authors: Liu Xiaojuan , Ban Zhuo , Yang Yingying , Xu Huihui , Cui Yifan , Wang Chenxue , Bi Quanxin , Yu Haiyan , Wang Libing
Published: August 2024

Yellowhorn (Xanthoceras sorbifolium Bunge) is an economically important tree species in northern China, mainly distributed in arid and semi-arid areas where water resources are scarce. Drought affects its yield and the expansion of its suitable growth area. It was found that the wax content in yellowhorn leaves varied significantly among different germplasms, which had a strong correlation with the drought resistance of yellowhorn. In this study, XsMYB30 was isolated from ‘Zhongshi 4’ of yellowhorn, a new highly waxy variety. DAP-Seq technology revealed that the pathways associated with fatty acids were significantly enriched in the target genes of XsMYB30. Moreover, the results of electrophoretic mobility shift assay, yeast one hybrid assay and dual-luciferase assay demonstrated that XsMYB30 could directly and specifically bind with the promoters of genes involved in wax biosynthesis (XsFAR4, XsCER1 and XsKCS1), lipid transfer (XsLTPG1 and XsLTP1) and fatty acid synthesis (XsKASIII), thus enhancing their expression. In addition, the overexpression of XsMYB30 in poplar promoted the expression levels of these target genes and increased the wax deposition on poplar leaves leading to a notable improvement in the plant’s ability to withstand drought. These findings indicate that XsMYB30 is an important regulatory factor in cuticular wax biosynthesis and the drought resistance of yellowhorn.
Junta Democrática: Californios and Reconstruction in California
Authors: Suárez Camille
Published: August 2024

During the Civil War and Reconstruction Era, elite Californios—Mexicans of mixed-race descent made citizens by the Treaty of Guadalupe Hidalgo—supported legislation and political platforms that rejected the varied attempts at biracial democracy. Through an examination of the political life of Antonio Coronel, this article reconsiders elite Californios as state makers and obstructors of Reconstruction in California. At the end of the U.S.-Mexico War and until his death in 1894, Coronel, like other Californios, collaborated with Anglo American politicians to maintain his regional power by supporting a racially restrictive state. In offering their cooperation, elite Californios momentarily maintained their privileged social status in areas where Californios held local political control, such as Los Angeles and Santa Barbara. While Anglo American settlers relied on elite Californios for political legitimacy and state making, they viewed Californios as unassimilable into whiteness because of their Spanish culture and mixed ancestry, and they gradually denied Californio claims to racial superiority and socio-legal privileges, as political cooperation became less crucial to the success of the state project. As a direct result of Coronel’s and other elite Californios’ cooperation before the U.S. Civil War (1861–1865) and through Reconstruction (1863–1879), the California government rejected the federal government’s experiment in biracial democracy and supported policies of white supremacy that targeted the state’s growing non-white populations, a rejection that eventually jeopardized Californio power, including Coronel’s. This article demonstrates that Californio participation was crucial to the state’s rejection of Reconstruction.
Genome Sequence Data of Pseudalkalibacillus hwajinpoensis MABIK MI00000821, an Inhibitor of Fumonisin Production in Fusarium fujikuroi
Authors: Shin Soobin , Lee Jin Woo , Lee Nahyun , Han Jae Woo , Choi Gyung Ja , Son Hokyoung , Kim Hun
Published: August 2024

Pseudalkalibacillus hwajinpoensis strain MABIK MI00000821 isolated from seawater exhibited inhibitory activity against the fumonisin production of Fusarium fujikuroi. Here, we report the draft genome sequence of the strain MABIK MI00000821 obtained using the PacBio RSII system. The genome comprises a single circular chromosome 4,369,347 bp in length, with an average GC content of 40.1%. Genome annotation predicted 4,351 protein-coding genes, 27 rRNA genes, and 89 tRNA genes. Moreover, the MABIK MI00000821 genome harbors five putative biosynthetic gene clusters responsible for secondary metabolites, including terpenes, a polyketide, and a siderophore. This genome sequence will contribute to a better understanding of the fumonisin inhibitory mechanism of the P. hwajinpoensis strain.

[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .