bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond simple vs. complex: exploring the nuanced and unexpected effects of spatial environmental complexity on mating patterns and female fecundity
Authors: Talagala Sanduni , Rakosy Emily , Long Tristan A F 
Published: July 2024

Abstract
The features of the physical environment set the stage upon which sexual selection operates, and consequently can have a significant impact on variation in realized individual fitness, and influence a population’s evolutionary trajectory. This phenomenon has been explored empirically in several studies using fruit flies (Drosophila melanogaster) which have found that changing the spatial complexity of the mating environment influenced male–female interaction dynamics, (re)mating rates, and realized female fecundities. However, these studies did not explore mating patterns, which can dramatically alter the genetic composition of the next generation, and frequently only compared a single, small “simple” environment to a single larger “complex” environment. While these studies have shown that broadly changing the characteristics of the environment can have big effects on reproductive dynamics, the plasticity of this outcome to more subtle changes has not been extensively explored. Our study set out to compare patterns of mating and courtship between large- and small-bodied males and females, and female fecundities in both a simple environment and 2 distinctly different spatially complex environments. We found that realized offspring production patterns differed dramatically between all 3 environments, indicating that the effects of increasing spatial complexity on mating outcomes are sensitive to the specific type of environmental complexity. Furthermore, we observed female fecundities were higher for flies in both complex environments compared those in the simple environment, supporting its role as a mediator of sexual conflict. Together, these results show that the union of gametes within a population can be greatly influenced by the specific spatial features of the environment and that while some outcomes of increased environmental complexity are likely generalizable, other phenomena such as mating patterns and courtship rates may vary from one complex environment to another.
Population genetic diversity and structure of Tephritis angustipennis and Campiglossa loewiana (Diptera: Tephritidae) based on COI DNA barcodes in the three-river source region, China
Authors: Zhang Li-Jun , Liu Ying , Wang Yan-Long , Xie Le-Le , Wang Xin-You , Ma Yu-Shou 
Published: July 2024

Abstract
Tephritis angustipennis (Diptera: Tephritidae) and Campiglossa loewiana (Diptera: Tephritidae) are phytophagous pests in China. Their damage has significantly impacted the collection and cultivation of germplasm resources of native Asteraceae plants. However, the genetic characteristics and structure of their population are unclear. This study focused on the highly damaging species of T. angustipennis and C. loewiana collected from the three-river source region (TRSR). We amplified the mitochondrial cytochrome C oxidase subunit I (mtCOI) gene sequences of these pests collected from this area and compared them with COI sequences from GenBank. We also analyzed their genetic diversity and structure. In T. angustipennis, 5 haplotypes were identified from 5 geographic locations; the genetic differentiation between France population FRPY (from Nylandia, Uusimaa) and China populations GLJZ (from Dehe Longwa Village, Maqin County), GLDR (from Zhique Village, Dari County), and GLMQ (from Rijin Village, Maqin County) was the strongest. GLJZ exhibited strong genetic differentiation from GLDR and GLMQ, with relatively low gene flow. For C. loewiana, 11 haplotypes were identified from 5 geographic locations; the genetic differentiation between the Chinese population GLMQ-YY (from Yangyu Forest Farm, Maqin County) and Finnish population FDNL (from Nylandia, Uusimaa) was the strongest, with relatively low gene flow, possibly due to geographical barriers in the Qinghai–Tibet plateau. Only 1 haplotype was identified across GLDR, GLMQ, and GLBM. High gene flow between distant locations indicates that human activities or wind dispersal may facilitate the dispersal of fruit flies and across different geographic. Geostatistical analysis suggested a recent population expansion of these 2 species in TRSR. Our findings provide technical references for identifying pests in the TRSR region and theoretical support for managing resistance, monitoring pest occurrences, analyzing environmental adaptability, and formulating biological control strategies for Tephritidae pests on Asteraceae plants.
Exploring the combined therapeutic efficacy of bexarotene and icariin in type 2 diabetic rats
Authors: Dik Burak , Parlak Tugba Melike , Ates Mehmet Burak , Tufan Oznur 
Published: July 2024

Abstract

Objectives
The aim of this study was to determine the single and combined antidiabetic activity and side effects of the retinoid X receptor agonist bexarotene and the thioredoxin-interacting protein inhibitor and peroxisome proliferator-activated receptor γ and AMP-activated protein kinase activator icariin.

Methods
The rats were grouped as healthy (control), diabetes, diabetes + bexarotene (20 mg/kg), diabetes + icariin (60 mg/kg), diabetes + bexarotene (10 mg/kg) + icariin (30 mg/kg) low-dose combination and diabetes + bexarotene (20 mg/kg) + icariin (60 mg/kg) high-dose combination groups.

Key findings
Icariin treatment led to a significant reduction in glucose levels compared with the diabetes control group, a remarkable outcome observed 45 days after the initial application. HbA1c levels of the icariin and low-dose combination treatment groups were significantly lower than in the diabetes group. Notably, icariin treatment also significantly elevated HOMA-β levels, which is indicative of improved β-cell function. Icariin significantly decreased glucose levels at 30 and 120 min in the oral glucose tolerance test. Moreover, it ameliorated hepatocyte degeneration, hepatic cord dissociation, congestion, mononuclear cell infiltration in the liver, and degeneration in the pancreas.

Conclusions
Icariin treatment exhibited robust antidiabetic effects with fewer side effects than other treatment options in this study. In future studies, long-term and varying doses of icariin will contribute to the development of novel antidiabetic drugs.
Development of a small shuttle plasmid for use in oral Veillonella and initial appraisal of potential for fluorescence-based applications
Authors: Goetting-Minesky M Paula , Kim Jordan , White Duane T , Hayashi Michael , Rickard Alexander H , Fenno J Christopher 
Published: July 2024

Abstract
Oral Veillonella species are among the early colonizers of the human oral cavity. We constructed a small, single-selectable-marker shuttle plasmid, examined its ability to be transformed into diverse oral Veillonella strains, and assessed its potential use for expressing a gene encoding an oxygen-independent fluorescent protein, thus generating a fluorescent Veillonella parvula strain. Because tetracycline resistance is common in Veillonella, we replaced genes encoding ampicillin- and tetracycline-resistance in a previously described shuttle plasmid (pBSJL2) with a chloramphenicol acetyltransferase gene. The resulting plasmid pCF1135 was successfully introduced into four strains representing V. parvula and V. atypica by either natural transformation or electroporation. We then modified this plasmid to express a gene encoding an oxygen-independent fluorescent protein in V. parvula SKV38. The resulting strain yielded a fluorescence signal intensity ∼16 times higher than the wild type in microplate-based fluorimetry experiments. While fluorescence microscopy demonstrated that planktonic cells, colonies, and biofilms of fluorescent V. parvula could also be imaged, photobleaching was a significant issue. In conclusion, we anticipate this genetic system and information provided here will facilitate expanded studies of oral Veillonella species’ properties and behavior.
Social network analysis of the Babylonian Talmud
Authors: Satlow Michael L , Sperling Michael 
Published: July 2024

AbstractThis article analyzes the citation network of the Babylonian Talmud, building on an earlier article that we published (Satlow and Sperling 2022). The article has three goals. Our first goal is to show how an ontological-based information extraction system combined with pattern matching can successfully extract structured data from a very complicated, unstructured text. Our second goal is to extend our previous analysis and demonstrate how citation data might lead to wider conclusions about redactional patterns. In addition to highlighting the citation tendencies of different tractates (which could indicate different redactors for those tractates), we hypothesize that there existed a source document originating in the circle of Rav Yehudah bar Yehezkel, used by at least some redactors, and that the character of Rabbi Zeira deserves further attention as an important figure connecting different nodes on the network. Finally, we seek to outline an analytical workflow that could be helpful to other historical projects in the digital humanities.
Diagnostic performance of the (1-3)-β-d-glucan assay in patients with different risks for invasive fungal diseases
Authors: Nham Eliel , Kim Si-Ho , Ko Jae-Hoon , Huh Kyungmin , Cho Sun Young , Kang Cheol-In , Chung Doo Ryeon , Peck Kyong Ran 
Published: July 2024

Abstract
We evaluated the diagnostic performance of the β-d-glucan (BDG) test (Beijing Gold Mountain River Tech) in diagnosing invasive fungal disease (IFD) and its variations among patients with different risks. Patients ≥18 years old who underwent a serum BDG test (positive cutoff value &gt;80 pg/ml) from April 2017 through May 2018 were collected consecutively. Patients were classified into three groups: group 1, patients with host factors as defined by the prior 2008 European Organization for Research and Treatment (EORTC) criteria; group 2, those with extended host factors in 2020 EORTC criteria; and group 3, those without any risk factor mentioned in the criteria. IFD was defined by 2020 EORTC criteria, but BDG was not considered. Diagnostic performance of the serum BDG test was measured by the area under the curve (AUC) of the receiver-operating characteristic curve. Among 469 patients, 15.4% (72/469) were diagnosed with IFD (48/191 [25.1%], 14/144 [9.7%], and 10/134 [7.5%] in groups 1, 2, and 3, respectively). The BDG assay showed fair performance (AUC 0.748 [95% CI: 0.688–0.810]). Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 77.8%, 60.7%, 26.4%, and 93.8%, respectively. PPV was higher in group 1, and NPV was higher in group 3. Additionally, diagnostic odds ratios were 6.73, 2.88, and 5.92 in groups 1, 2, and 3. Immunosuppressant use, non-IFD/Candida colonization, and central venous catheter were associated with false positivity. Clinicians should cautiously interpret the BDG assay, considering the various diagnostic performances depending on the different levels of risk.
Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data
Authors: Thiel Bernhard C , Bussi Giovanni , Poblete Simón , Hofacker Ivo L 
Published: July 2024

Abstract
The determination of the three-dimensional structure of large RNA macromolecules in solution is a challenging task that often requires the use of several experimental and computational techniques. Small-angle X-ray scattering can provide insight into some geometrical properties of the probed molecule, but this data must be properly interpreted in order to generate a three-dimensional model. Here, we propose a multiscale pipeline which introduces SAXS data into modelling the global shape of RNA in solution, which can be hierarchically refined until reaching atomistic precision in explicit solvent. The low-resolution helix model (Ernwin) deals with the exploration of the huge conformational space making use of the SAXS data, while a nucleotide-level model (SPQR) removes clashes and disentangles the proposed structures, leading the structure to an all-atom representation in explicit water. We apply the procedure on four different known pdb structures up to 159 nucleotides with promising results. Additionally, we predict an all-atom structure for the Plasmodium falceparum signal recognition particle ALU RNA based on SAXS data deposited in the SASBDB, which has an alternate conformation and better fit to the SAXS data than the previously published structure based on the same data but other modelling methods.
Association of personalized and tumor-informed ctDNA with patient survival outcomes in pancreatic adenocarcinoma
Authors: Botta Gregory P , Abdelrahim Maen , Drengler Ronald L , Aushev Vasily N , Esmail Abdullah , Laliotis George , Brewer Chris M , George Giby V , Abbate Steven M , Chandana Sreenivasa R , Tejani Mohamedtaki A , Malla Midhun , Bansal Dhruv , Rivero-Hinojosa Samuel , Spickard Erik , McCormick Nicole , Cecchini Michael , Lacy Jill , Fei Naomi , Kasi Pashtoon Murtaza , Kasi Anup , Dayyani Farshid , Hanna Diana L , Sharma Shruti , Malhotra Meenakshi , Aleshin Alexey , Liu Minetta C , Jurdi Adham 
Published: July 2024

Abstract

Introduction
Personalized and tumor-informed circulating tumor DNA (ctDNA) testing is feasible and allows for molecular residual disease (MRD) identification in patients with pancreatic ductal adenocarcinoma (PDAC).

Methods
In this retrospective analysis of commercial cases from multiple US institutions, personalized, tumor-informed, whole-exome sequenced, and germline-controlled ctDNA levels were quantified and analyzed in patients with PDAC. Plasma samples (n = 1329) from 298 clinically validated patients were collected at diagnosis, perioperatively (MRD-window; within 2-12 weeks after surgery, before therapy), and during surveillance (&gt;12 weeks post-surgery if no ACT or starting 4 weeks post-ACT) from November 2019 to March 2023.

Results
Of the initially diagnosed patients with stages I-III PDAC who went for resection, the median follow-up time from surgery was 13 months (range 0.1-214). Positive ctDNA detection rates were 29% (29/100) and 29.6% (45/152) during the MRD and surveillance windows, respectively. Positive ctDNA detection was significantly associated with shorter DFS within the MRD window (median DFS of 6.37 months for ctDNA-positive vs 33.31 months for ctDNA-negative patients; HR: 5.45, P &lt; .0001) as well as during the surveillance period (median DFS: 11.40 months for ctDNA-positive vs NR for ctDNA-negative; HR: 12.38, P &lt; .0001). Additionally, DFS was significantly better with KRAS wildtype status followed by KRASG12R (HR: 0.99, P = .97), KRASG12D (HR: 1.42, P = .194), and worse with KRASG12V (HR: 2.19, P = .002) status. In multivariate analysis, ctDNA detection at surveillance was found to be the most significant prognostic factor for recurrence (HR: 24.28, P &lt; .001).

Conclusions
Perioperative tumor-informed ctDNA detection in PDAC is feasible across all stages and is associated with patient survival outcomes.
The Sovereign Lives of India and Pakistan
Authors: Mishra Atul 
Published: July 2024

Abstract
Sovereign Lives explores what it has meant for India and Pakistan to act as sovereign states that became entangled at birth by an unsatisfactory partition. Sovereignty is conventionally understood as a means to achieve the goals that states set for themselves. This book argues that for India and Pakistan, sovereignty has become an end in itself, and that its pursuit has aided majoritarianism, insecurity, ideological conflict, and mutual estrangement that adversely affect the two states as well as their peoples. The book examines the trajectory of three problems that the partition of 1947 bequeathed to the two states. It investigates the state–minority relations, national identity debates, and contestation over Kashmir to outline the parallel processes of minoritization, homogenization, and territorialization. It shows how these processes signify the two states’ quest for sovereignty. The scholarship on India and Pakistan often privileges their bilateral relations. In contrast, this book carries out the deeper task of a single-frame analysis and critique of their intertwined statehoods. Ultimately, the book shows the inadequacy of the nation state form as the basis for political community in the subcontinent. It concludes by pointing to the contemporary relevance of alternative ideas of sovereignty and political community in South Asia that were articulated during the first half of the twentieth century.
American Popular Music and Its Business in the Digital Age
Authors: Sanjek Rick 
Published: July 2024

Abstract
This book is a sequel to my father’s American Popular Music and its Business—the First 400 Years, also published by Oxford University Press. It compares the music business to a funnel through which money spent by consumers and licensees flows before reaching performers and songwriters after deducting the cost of financing, managing, promoting, and marketing. It also traces how the delivery of music transitions from analog vinyl and tape to digital successors from CDs through MP3s, to subscription streaming. It follows the Big Six major label groups consolidating to the Big Three by 2020, and the merger of Live Nation and Ticketmaster completing the transition of ticketing from paper to electronic to digital. Technology including the internet, smartphones, broadband, and social media platforms facilitated the management of the metadata emanating from the all-important relationship between consumers and creators, for without this relationship, there is no music business. The book has three main sections spanning 1985 to 1995, 1996 until 2006, and 2007 through 2019. Each has five chapters starting with “The Game of Musical Thrones” about the competition between record labels. “Records, Retail, Radio, and the Charts That Bind Them” examines the revenue generated by record sales and radio airplay. Then comes “Publishing, Copyright, Legislation, and Litigation,” “The Creators of Music—Getting Paid,” and “The Consumer—From Whom, How, and Where the Money Flows,” Finally an epilogue covers the effects of COVID-19 in 2020 on all involved, closing with a glimpse into the crystal ball of the digital future.
Records, Radio, Retail, Streaming, and the Charts
Authors: Sanjek Rick 
Published: July 2024

Abstract
Record revenue continued to fall through the 2008 recession, settling at $7 billion for 2010 through 2015. In 2010 Charlie Anderson, CEO of Anderson Merchandisers, chief supplier to Walmart, predicted the demise of the CD as a viable retail product within six years. Spotify launched in the US in 2011. Apple Music followed in 2015. As downloads, and then streaming, replaced revenue from retail sales, Billboard adjusted its chart formulas accordingly. Leading retail distributor Alliance diversified into other music products. Record Store Day promoted the growing vinyl revival. SiriusXM invested in and then acquired Pandora with plans to maximize their synergistic potential. In 2019 record revenue reached $11.4 billion with 79.5 percent from streaming, and only 10.1 percent from retail. Streaming had led the industry to recovery, retail bin space had been reduced to superstars and vinyl, and radio revenue had fallen by a third but still dominated in-car listening.
Not All Wounds Are Visible
Authors: Hammond Louisa 
Published: July 2024

Abstract
I live and work in Manchester, UK, and studied Visual Arts at the University of Salford, from which I graduated in 2008. Since that time, I have been creating artwork and exhibiting in a variety of galleries, festivals, and public spaces. Getting involved in art-based projects around the destigmatization of mental illness is close to my heart. I was unexpectedly diagnosed with schizoaffective disorder in 2010, which became a very dramatic, turbulent time in my life. During my recovery, I was referred to art therapy sessions using a variety of media, including textiles. It was at these workshops at an art-for-health National Health Service (NHS) organization that I was inspired to begin producing artwork again. I feel that my practice has very much been impacted and inspired by this life-changing experience, and I aim to voice my knowledge of living with mental illness through what I create.
In Chiron’s Footsteps
Authors: Williams Paula J 
Published: July 2024

Abstract
I have always been drawn to the concept of the wounded healer, an idea going back to Greek mythology and developed as an archetype by Jung. It centers around Chiron, a centaur who is wounded in battle by an arrow dipped in Hydra’s blood. He embarks upon a journey to try to find a way to heal the terrible pain of his injury; as he travels, seeking his cure, he teaches others the art of healing. In so doing, he finds his own healing, learning to understand others’ pain from his own experience of pain. This idea is comforting to me as it removes the pressure to have healed myself before I can help others to heal, and it helps me make sense of my own path.
The Lived Experience of LGBT Veterans
Authors: Wagner Kathryn 
Published: July 2024

Abstract
The Tuesday following the Orlando shooting I walked into my psychotherapy group and was greeted with tears and silence. This was the LGBT Group for Veterans, run by myself and another co-leader at a VA hospital on the East Coast. Most members didn’t know what to say and many were openly crying. “Shocked,” “sad,” and “fear” were just a few words these veterans used to describe their feelings. Throughout the hour, my patients expressed strong reactions to Orlando, remembering their own experiences of being stigmatized and even assaulted within the military for being lesbian, gay, bisexual, or transgender. Our discussion also touched on racial dynamics, both within Orlando and the group itself. A few of the older veterans in my group, who had come out later in life, were not aware about safe spaces for LGBT people of color, such as the dance club where the shooting took place; these men appreciated learning from other members in the group about why such spaces were important. This particular group was populated with four gay men, two lesbians, a transgender man, and two transgender women. While not a veteran, I am queer, gender-nonconforming, and disabled—identities about which I talk openly in the
Problem Glyphs
Authors: Gauger Eliza 
Published: July 2024

Abstract
Problem Glyphs is a sort of occult advice column. I’m an illustrator by trade, but, four years ago, I started drawing sigils for people who sent me their problems. I tried to get at the crux of their issues; if I didn’t have any useful advice, I just tried to be encouraging. The drawings did a lot of the work for me because they changed every time someone different looked at them: common symbols are personally interpreted in entirely subjective ways, and the sparse text (just a title) conveyed a meaning but did not force the interpretation. The early ones were very simple; the later ones more complex and illustrative.
When the Levee Breaks
Authors: Ostovar Afshon 
Published: July 2024

Abstract
This chapter discusses how the attacks of 9/11 prompted the Bush administration to embark on an ambitious effort to remake the Middle East through the war in Iraq. The administration’s initial response to 9/11 was the war in Afghanistan, which inspired a brief diplomatic exchange between the United States and Iran—one that collapsed following Bush’s infamous “axis of evil” speech. The prospect of war in Iraq triggered a crisis among Arab states which sought a way to avoid it—an effort that failed due to the disunity and acrimony of Arab leaders. The invasion of Iraq was successful, but the occupation quickly stumbled. Controversial policies such as de-Baathification helped fuel insurgency among disaffected Sunni Arabs, and Muqtada al-Sadr inspired Shia followers to resist the occupation. The Mahdi Army’s failed uprising created an opportunity that Iran would quickly seize.