bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract IA014: BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair
Authors: Lim Pei Xin , Jasin Maria 
Published: January 2024

Abstract
Tumor suppressor BRCA2 functions in multiple pathways. The role of BRCA2 in homologous recombination, also termed homology-directed repair (HDR), is particularly well known. We also showed that it has a key role in the protection of stalled replication forks from the MRE11 nuclease. Moreover, BRCA2 also suppresses the formation of single-stranded gaps during replication. We have attempted to delineate the relative contributions of these three pathways to the maintenance of genome integrity and chemotherapy response using separation of function alleles. First, we report that mouse and human cells require a RAD51 filament stabilization motif in BRCA2 for both fork protection and gap suppression but not HDR. In mice, loss of fork protection and gap suppression do not compromise genome instability or shorten tumor latency. By contrast, HDR deficiency increases spontaneous and replication stress-induced chromosome aberrations and tumor predisposition. Unlike with HDR, fork protection and gap suppression defects are also observed in Brca2 heterozygous cells from mice, likely due to reduced RAD51 stabilization at stalled forks and gaps. Sensitivity to the PARP inhibitor olaparib is greatest for HDR-deficient cells, although fork protection/gap suppression-defective cells show a weak sensitivity. Gaps arise from PRIMPOL activity, which is associated with sensitivity to 5-hydroxymethyl-2’-deoxyuridine (hmdU) and DNPH1 inhibition due to the formation of SMUG1-generated abasic sites and is exacerbated by poly(ADP-ribose) polymerase inhibition. In summary, this work demonstrates that HDR deficiency has the major role in generating sensitivity to chemotherapeutics, although gap suppression deficiency may be targeted by specific agents.
Citation Format: Pei Xin Lim, Maria Jasin. BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr IA014.
Abstract PR010: Understanding extrachromosomal telomere generation in ALT cancers
Authors: Lee Junyeop , Lee Jina , Sohn Eric J. , Taglialatela Angelo , O’Sullivan Roderick J. , Ciccia Alberto , Min Jaewon 
Published: January 2024

Abstract
Introduction: Alternative Lengthening of Telomeres (ALT) is a telomere maintenance mechanism mediated by break-induced replication (BIR), evident in approximately 15% of human cancers. A characteristic feature of ALT cancers is the presence of C-circles, circular single-stranded telomeric DNAs composed of Cytosine-rich (CCCTAA) sequences. These C-circles are unique biomarkers of ALT cells and may be generated from extrachromosomal telomeric single-stranded DNAs (ssDNAs), also unique to ALT cells, but the generation process remains undefined. Methods and results: In order to investigate C-rich ssDNA, we developed a highly sensitive method to detect single stranded telomeric DNA, called 4SET (Strand-Specific Southern-blot for Single-stranded Extrachromosomal Telomeres) assay. Utilizing 4SET, we are able to capture C-rich single stranded DNAs that are near 200 to 1500 nucleotides in size. Both telomeric ssDNAs and C-circles are abundant in cytoplasm and nucleoplasm fractions, which supports the hypothesis that telomeric ssDNA accumulation may indeed precede C-circle formation. We also found that telomeric ssDNAs originate during Okazaki fragment processing during C-rich lagging strand DNA synthesis at telomere ends during telomere elongation in ALT cancers. During lagging strand priming and synthesis, the CST-PP complex (CTC1/STN1/TEN1-PRIMASE-Polymerase alpha) primes the telomeric C-rich strand; then, Polymerase delta and BLM helicase facilitate excessive strand displacement, leading to the accumulation of telomeric ssDNAs in the nucleoplasm and cytoplasm which is potential precursor material for C-circles in ALT cancers. Conclusion: Here, we introduce a highly sensitive 4SET method for studying telomeric ssDNA, which we used to propose a new model for the generation of telomeric C-rich ssDNAs and C-circles during ALT-mediated telomere elongation. Our work contributes to a growing body of knowledge pertaining to the idiosyncrasies of the ALT mechanism based on investigation of its unique biomarkers.
Citation Format: Junyeop Lee, Jina Lee, Eric J. Sohn, Angelo Taglialatela, Roderick J. O’Sullivan, Alberto Ciccia, Jaewon Min. Understanding extrachromosomal telomere generation in ALT cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr PR010.
EVALUATION OF REVEGETATION PRACTICES IN POST-MINED AREAS OF INDONESIA
Authors: Wijayanti Meilina , Kapp Gerald , Mansur Irdika 
Published: January 2024

In compliance with government regulations, mining companies in Indonesia are obliged to reclaim and return a post-mined area into its pre-mining condition. Revegetation, as part of reclamation activity, performs a significant role in the rehabilitation of degraded post-mined areas to restore their productive land uses. Hence, this study aimed to assess tree growth on the reclamation sites across four mining companies in East Kalimantan, South Sulawesi, South Sumatra, and West Java in Indonesia and to evaluate whether the companies have met the legal requirements set for site revegetation. The success parameters were based on the applicable regulations of the Ministry of Environment and Forestry (MOEF) P.60/Menhut-II/2009 and tree growth parameters (stem diameter, total height and basal area). The parameters set by MOEF included revegetation realization, survival rate, tree density, tree health, species composition and rotation length. The four mining companies applied the two-phase planting method that included the planting of Enterolobium cyclocarpum for the first phase; and in the second phase, the slow growing native species, such as Intsia palembanica, Sycygium polyanthum, Shorea spp. and Elmerrillia tsiampaca. The tree growth parameters showed different performances over species and reclaimed sites. An extremely high growth of stem basal area of 57.6 m2/ha in 11 years, was recorded in the E. tyclocarpum stand of the Mining Company in South Sulawesi. All four mining companies strived to comply with the regulation with scores of revegetation success ranging from 15 to 25 out of 25 possible points. However, these favorable results may not be representative of all the mining companies, as the ones assessed were only those voluntarily supporting this research. Moreover, each of the four companies made some distinct efforts in implementing post-mining revegetation, such as by establishing plots of Melaleuca cajuputi trees producing cajuput oil and polycultures of native species.Â Â Keywords: mining, reclamation, reforestation, rehabilitation, success parametersÂ Â Â Â Â
AGRONOMIC TRAITS OF LOCAL WETLAND RICE VARIETIES IN JAMBI PROVINCE
Authors: Bobihoe Julistia 
Published: January 2024

Swamp Â land is one of the areas of agricultural Â development Â that is perspective Â where the agroecosystem Â has the characteristics, Â and very unique with specific inundation and soil properties compared to other agroecosystems. Â At present, in some of these areas rice cultivation Â is still using local varieties. Local Â rice is one of the genetic resources which is quite diverse. The ability to adapt to extreme environments Â is the reason for most farmers to continue to plant and cultivate local Â rice. The study of the agronomic traits of local rice in swamp land is carried out in order to see the agronomic character and obtain varieties that have superior traits based on their agronomic character. The research activity was carried out in the Rantau Kapas Mudo Village, Batanghari Regency, Jambi Province from April to October 2016. The study used a single plot method. The local rice varieties used are genetic resources of swamp land rice planted in single plots measuring 10 m x 5 m, the distance between plots is 1 m with a spacing of 25 cm x 25 cm. The local varieties used were as many as 11 varieties, consisting of: Serendah Halus, Rimbun Daun, Karya, Serendah Bawang, Sereh Aek, Botol, Pontianak, Semut, Dawi, Ketan Itam and D.I. The characters observed consisted of plant height at harvest, number of productive tillers, age of harvest, number of grains per panicle, number of filled grains per panicle, number of empty grains per panicle, weight of 1,000 grains, seed shape and production. The results showed that there were differences between the local rice varieties of swamp land observed. The results showed that the highest production (3.32 tons / ha) was found in the Leafy variety, evidenced by the Dawi variety (2.86 t / ha). The results showed that there were two local rice varieties, Rimbun Daun and Dawi which had the potential to be developed and were expected to become the leading regional rice varieties in the swamp land.
KARAMUNTING (Melastoma malabathricum) EXTRACTS ON WHITE SHRIMP (Litopenaeus vannamei) MATURITY
Authors: Ridwan Ahmad , Awaludin Awaludin 
Published: January 2024

Lanosterol is a phytosterol that is used by crustacea to form animal steroid hormone that plays a role in the reproduction of the shrimp. This research aims to determine the response of ovary development in white shrimp parent after given Karamunting ethanol extract. This research was carried out in several stages: 1. Injecting the white shrimp every 3 days, at the base of the 5th leg, for 15 days with variable control dose 0 (C), 10 mg / kg BW (T1), 7.5 mg / kg BW (T2), 5 mg / kg BW (T3), 2 mg / kg BW (T4) and 1 mg / kg BW (T5), (2). Isolation of white shrimp parent ovary, (3). Measurement of progesterone level in the ovary using the Radioimmunoassay (RIA) method, (4) Histology of white shrimp parent ovary, and (5). Data analysis. The statistical results of measuring the increase in progesterone showed that administration of ethanol extract of karamunting at the end of maintenance had a significant difference (PË‚0.05). Histology observations of gonadal development in control, T5 and T4 showed cells to develop to previtellogenesis oocytes whereas in treatment T1, T2 and T3 ovary cells developed into endogenous vitellogenesis oocytes and only in T1 ovarian cells developed to form exogenous vitellogenesis oocytes. Â Statistical results of oocyte size after administration of the karamunting extract at the end of maintenance were significantly different (PË‚0.05). The average oocyte size at the beginning of maintenance (15.57 Â± 3.15 Âµm), C (25.29 Â± 2.69 Âµm) indicating that at the end of the ovarian treatment development occurred both in control and treatment. T1 (65.65 Â± 2.64 Âµm), T2 (63.98 Â± 3.06 Âµm), T3 (39.12 Â± 6.01 Âµm), T4 (28.08 Â± 0.84 Âµm) and T5 (27.65 Â± 0.71 Âµm) also appear to be greater than the oocyte size at the beginning of maintenance and control. Based on the results of this study it can be concluded that the content of lanosterol in karamunting plants can increase the hormone progesterone which indicates an acceleration of gonadal maturity and enlargement of oocyte size in the parent shrimp of White shrimp.
Change from the COVID-19 Pandemic to a New Normal: Documenting Consumption Behavior of Two Years with Big Data
Authors: Konishi Yoko , Saito Takashi , Kanai Hajime , Igei Naoya , Mizumura Junichi , Shiga Kyoko , Sueyasu Keita , Hamaguchi Ryosuke 
Published: January 2024

Abstract
The COVID-19 pandemic has drastically changed our daily lives in terms of eating, learning, working, and leisure time. So far, Japan has experienced eight waves of widespread infection and three emergency declarations but has coped with the crisis without mandatory lockdowns, behavioral restrictions, and mandatory mask-wearing that were seen in other countries. The response has mainly been an encouragement of behavioral changes in our daily lives. In this paper, we observe through “consumption big data” the initial disruption, the adaptation period, and the change to a new normal. We use point of sale (POS) data from supermarkets, convenience stores, home centers, drugstores, and consumer electronics mass merchandisers, as well as data from household bookkeeping applications, for the two years from January 2020 to December 2021. The POS data were used to observe item-level sales trends, while the household bookkeeping application data were used to observe trends in service expenditures and the prevalence of cashless payments. This made it possible to comprehensively understand the changes in consumer behavior during the pandemic.
Steinernema yirgalemense (Steinernematidae) to control Phlyctinus callosus and Phlyctinus xerophilus (Curculionidae)
Authors: Hansen Steffan P. , Malan Antoinette P. , Haran Julien M. , Dunn Murray D. , Addison Pia 
Published: January 2024

Summary
Considerable progress has been made in the surveying, taxonomy, screening, mass production and formulation of entomopathogenic nematodes (EPN) and their associated symbiotic bacteria in South Africa. Steinernema yirgalemense isolate 157-C is one of the most promising native EPN candidates with regards to virulence, its broad insect-host spectrum, and can be readily mass-produced and formulated into a commercial product. The banded fruit weevils, Phlyctinus callosus sensu stricto and Phlyctinus xerophilus, previously grouped together under the Phlyctinus callosus sensu lato species concept, are native entimine weevils of economic importance to deciduous fruit, grapevine and berries in the Western Cape province of South Africa. This study investigated potential differences in baseline susceptibility of larvae and pupae of the two weevil species to S. yirgalemense in laboratory screenings. The test arena used was 24-well bioassay plates, with an inoculation concentration of 200 infective juveniles (IJ) insect−1 for larvae and 100 IJ insect−1 for pupae. Infection was determined 48 h and 96 h after inoculation. Field-efficacy of S. yirgalemense, applied at a concentration of 60 IJ cm−2, against larvae of the two weevil species was determined in an ecologically relevant semi-field trial. In all cases in vitro mass-produced IJ of S. yirgalemense were used. No baseline differential susceptibility between P. callosus and P. xerophilus larvae was obtained in laboratory screenings. Phlyctinus pupae were approximately twice as susceptible compared to larvae, with significant differences between bioassay batches. Approximately 45% control of P. xerophilus larvae was obtained after 96 h of exposure to S. yirgalemense in the field, differing significantly from the control and P. callosus treatment. Low levels of Phlyctinus larval infection by native EPN (confirmed as Heterorhabditis bacteriophora from one P. xerophilus cadaver) occurred in both control and EPN treatment groups under field conditions.
Marx’s Critical Theory of Slavery
Authors: Best Beverley 
Published: January 2024

Abstract
Marx’s critical theory of slavery is the operational subtext throughout his critique of political economy. For Marx, the movement from modern slavery to capital represents a historical transition of significance, not only (or foremost) as an empirical transition but also as a transformation of social substance. Marx reveals why, in retrospect, production based on slavery, as logical configuration, must give way to the generalising logic of wage labour. Marx’s critical theory of slavery historicises wage labour (qua category) as the dissolution and inversion of enslaved labour (qua category). Plantation slavery production in the colonised territories initiates a qualitative development that constitutes the historical condition for the emergence of a mode of sociality that we can call ‘value’. Marx’s theoretical account of modern slavery is a lever in his broader critique of capital and is fundamentally distinct from empirical, historical accounts.
Clinical tools for evaluating the severity of overactive bladder: A systematic review of psychometric properties
Authors: Ali Mohammed Usman , Winser Stanley John , Kannan Priya , Kranz Georg S , Fong Kenneth Nai-Kuen 
Published: January 2024

Objectives To systematically evaluate the evidence describing the psychometric properties of clinical measures for assessing overactive bladder symptoms (urinary urgency with or without urge urinary incontinence, urinary frequency and nocturia). To evaluate the quality of this evidence-base using the COnsensus-based Standards for selecting health status Measurement INstruments (COSMIN) checklist and the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) tools. Data sources Five electronic databases (CINAHL, EMBASE, MEDLINE, Scopus and Web of Science) were searched from dataset inception to August 2023. Review methods Study screening, data extraction and quality appraisal were performed by two independent authors. Inclusion criteria were studies testing one or more psychometric properties of clinical tools for the assessment of overactive bladder symptoms among adults aged 18 years and older for both sexes. The methodological quality and quality of the evidence were evaluated using the COSMIN checklist and GRADE tools, respectively. Results The search identified 40 studies totalling 10,634 participants evaluating the psychometric properties of 15 clinical tools. The COSMIN methodological quality was rated good for most measures, and the GRADE quality of evidence ranged from low (13%) to high (33%). The Overactive Bladder Symptom Score, Overactive Bladder Questionnaire and Neurogenic Bladder Symptom Score were of good methodological and high-GRADE evidence qualities. Conclusion Overactive Bladder Symptom Score, the Overactive Bladder Questionnaire and the Neurogenic Bladder Symptoms Score are promising psychometrically sound measures. The Overactive Bladder Symptom Score has been applied to the most culturally diverse populations supported by studies of good methodological and high-GRADE evidence quality.
Assessing the efficacy of VerifyNow platelet-function testing in predicting postoperative hemorrhagic complications of neuroendovascular surgery: A systematic review and meta-analysis (part 2)
Authors: Mitchell Devon L , McGuire Laura Stone , Khalid Syed I , Alaraj Ali 
Published: January 2024

Background Dual antiplatelet therapy is used to reduce the risk of thromboembolic complications in neuroendovascular surgery. However, the predictive utility of preoperative platelet-sensitivity testing for decreasing bleed risk in patients undergoing endovascular neurointervention remains unclear. Objective We conducted a systematic review and meta-analysis to illustrate the association between platelet response and risk of hemorrhagic complications from neuroendovascular surgery, examine the efficacy of the VerifyNow platelet reactivity unit (PRU) assay in predicting hemorrhagic outcomes, and assess whether a clinically useful threshold for platelet response can be defined to standardize guidelines. Methods PubMed, Embase, and Scopus were searched. Articles were screened for relevance by title and abstract, followed by full text. Results Of 735 resultant articles, 17 studies of 2084 patients undergoing neuroendovascular intervention were included. Diagnoses included both intracranial and extracranial pathologies, of which 37.8% were treated with flow diversion, 22.4% with stent-assisted coil embolization, 14.3% with intracranial stenting, 12.8% with simple coil embolization, 5.8% with balloon-assisted coil embolization, 2.0% with extracranial stenting, and 4.8% with an alternate method. Precisely, 52.9% (9 out of 17) of studies determined platelet hyperresponse to be an independent predictor of postoperative hemorrhagic complications, with 11.8% (2 out of 17) of studies reporting a similar but non-statistically significant trend. 35.3% (6 out of 17) of studies found no relationship between platelet response and postoperative hemorrhagic complications. The estimated clinical threshold for PRU to prevent hemorrhagic complications varied considerably across studies (range: <46–118 PRU). Meta-analysis found platelet hyperresponse to have more than a 3-fold increased risk of hemorrhagic complications compared to normoresponders (relative risk = 3.2, p = 0.001). Conclusion Although this meta-analysis shows the predictive utility of the P2Y12 assay for postoperative hemorrhagic complications in neuroendovascular surgery, the optimal therapeutic threshold for minimizing bleeding risk is still uncertain. To better understand the utility of the P2Y12 assay in the perioperative period, further prospective research is needed.
Distinct peripheral T-cell and NK-cell profiles in HGBL-MYC/BCL2 vs patients with DLBCL NOS
Authors: de Jonge A. Vera , Duetz Carolien , Bruins Wassilis S. C. , Korst Charlotte L. B. M. , Rentenaar Rosa , Cosovic Meliha , Eken Merve , Twickler Inoka , Nijland Marcel , van der Poel Marjolein W. M. , de Heer Koen , Klerk Clara P. W. , Strobbe Leonie , Oosterveld Margriet , Boersma Rinske , Koene Harry R. , Roemer Margaretha G. M. , van Werkhoven Erik , Chamuleau Martine E. D. , Mutis Tuna 
Published: January 2024

Abstract
Patients with high-grade B-cell lymphoma with MYC and BCL2 rearrangements (HGBL-MYC/BCL2) respond poorly to immunochemotherapy compared with patients with diffuse large B-cell lymphoma not otherwise specified (DLBCL NOS) without a MYC rearrangement. This suggests a negative impact of lymphoma-intrinsic MYC on the immune system. To investigate this, we compared circulating T cells and natural killer (NK) cells of patients with HGBL-MYC/BCL2 (n = 66), patients with DLBCL NOS (n = 53), and age-matched healthy donors (HDs; n = 16) by flow cytometry and performed proliferation, cytokine production, and cytotoxicity assays. Compared with HDs, both lymphoma subtypes displayed similar frequencies of CD8+ T cells but decreased CD4+ T cells. Regulatory T-cell (Treg) frequencies were reduced only in patients with DLBCL NOS. Activated (HLA-DR+/CD38+) T cells, PD-1+CD4+ T cells, and PD-1+Tregs were increased in both lymphoma subtypes, but PD-1+CD8+ T cells were increased only in HGBL-MYC/BCL2. Patients with DLBCL NOS, but not patients with HGBL-MYC/BCL2, exhibited higher frequencies of senescent T cells than HDs. Functional assays showed no overt differences between both lymphoma groups and HDs. Deeper analyses revealed that PD-1+ T cells of patients with HGBL-MYC/BCL2 were exhausted with impaired cytokine production and degranulation. Patients with DLBCL NOS, but not patients with HGBL-MYC/BCL2, exhibited higher frequencies of NK cells expressing inhibiting receptor NKG2A. Both lymphoma subtypes exhibited lower TIM-3+– and DNAM-1+–expressing NK cells. Although NK cells of patients with HGBL-MYC/BCL2 showed less degranulation, they were not defective in cytotoxicity. In conclusion, our results demonstrate an increased exhaustion in circulating T cells of patients with HGBL-MYC/BCL2. Nonetheless, the overall intact peripheral T-cell and NK-cell functions in these patients emphasize the importance of investigating potential immune evasion in the microenvironment of MYC-rearranged lymphomas.