bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated microbiomics and metabolomics analysis reveals the influence of gut microbiota on the growth and metabolism of sea cucumber seedlings
Authors: Jia Airong , Niu Xinyan , Zhang Miansong , Liu Xue , Cui Tingting , Liu Changheng , Bai Xinfeng 
Published: January 2024

Abstract

Aims
This study explores the impact of gut microbiota on body metabolites and the growth rate of sea cucumber seedlings.

Methods and results
A comprehensive analysis using metabolomics and microbiomics was conducted to ascertain the gut microbiota and body metabolites in sea cucumber seedlings exhibiting varying growth rates. Distinct changes in the intestinal flora were observed in correlation with different growth rates of sea cucumber seedlings. The microbial communities of faster-growing seedlings exhibited greater diversity and evenness of taxa. For example, the abundance of genera Rhodococcus, Woeseia, Lysobacter, Desulfuromonadia_Sva1033, and Flavobacteriaceae_NS5_marine_group was more than 24 times higher in the fast-growing group compared to the slow-growing group. Metabolomics analysis revealed an association between high growth rates of cucumber seedlings and discrepancies in metabolites, such as amino acids, lipids, and carbohydrates. Isorenieratene, possibly synthesized by Rhodococcus, was more than 2.5 times more abundant in the fast-growing group than the slow-growing group. Slow-growing seedlings showed considerable enrichment of environmental pollutants, such as antibiotics and drugs, while their colonies were devoid of bacteria capable of degrading such pollutants. In addition, significant differences were observed between groups in the biosynthesis of amino acids, metabolism of arginine and proline, biosynthesis of unsaturated fatty acids, and metabolism of linoleic acid. Moreover, significant correlations between the microbial genera and sea cucumber metabolites were identified through correlation analysis.

Conclusions
Significant differences exist in the gut microbiota and metabolite composition among seedlings with varying growth rates. Microbes residing in the gut have the potential to influence the growth of seedlings through modulation of their metabolism.
Impaired muscle parameters in adults with mild to severe types of osteogenesis imperfecta: a cross-sectional study
Authors: Coussens Marie , Lapauw Bruno , De Wandele Inge , Malfait Fransiska , Pocovi Natasha C , Pacey Verity , Calders Patrick 
Published: January 2024

Abstract
Impaired muscle parameters may further compromise the already compromised skeleton in individuals with OI. This cross-sectional study aimed to compare muscle function and body composition in adults with various OI types and healthy controls. Sixty-eight adults with OI (mean age 42.2 yr; 27 men) and 68 healthy age- and sex-matched controls were recruited. Maximal isometric muscle force was assessed by handheld dynamometry (hand grip, hip flexors, shoulder abductors, and ankle dorsiflexors), muscle endurance by posture maintenance tests (shoulder abduction, hip flexion, and wall sit), and functional lower limb strength by 30-s chair rise test. In a sub cohort, dynamic muscle function (peak power and force) was assessed by a ground reaction force plate, and lean and fat mass, muscle and fat cross-sectional area (CSA), and muscle density by dual-energy X-ray absorptiometry and peripheral quantitative computed tomography. Multiple linear regression models were fitted with group (OI type I, III, IV/V, or controls), country, sex, and age in the fixed effects part. Overall, adults with various types of OI had lower isometric, endurance, and functional muscle strength (mean difference [MD] = OI type I: 19–43%, OI type IV/V: 25–68%, OI type III: 20–72%) compared to controls. Furthermore, adults with OI type I had lower dynamic muscle function (peak force [MD = 25–29%] and power [MD = 18–60%]), lean mass (MD = 10–17%), muscle CSA (MD = 9–21%), and muscle density (MD = 2–3%) but higher adiposity indices (MD = 24–42%) compared to controls. Functional lower limb strength and maximal muscle force were significantly different between OI types, whereas muscle endurance was not.
To conclude, adults with OI present with markedly impaired muscle function which may partially be explained by their altered body composition. Our findings emphasize the need for proper assessment of various muscle parameters and (research into) appropriate and safe muscle strengthening approaches in this population.
Influence of vitamin D supplementation on bone mineral content, bone turnover markers, and fracture risk in South African schoolchildren: multicenter double-blind randomized placebo-controlled trial (ViDiKids)
Authors: Middelkoop Keren , Micklesfield Lisa K , Walker Neil , Stewart Justine , Delport Carmen , Jolliffe David A , Mendham Amy E , Coussens Anna K , van Graan Averalda , Nuttall James , Tang Jonathan C Y , Fraser William D , Cooper Cyrus , Harvey Nicholas C , Hooper Richard L , Wilkinson Robert J , Bekker Linda-Gail , Martineau Adrian R 
Published: January 2024

Abstract
Randomized controlled trials (RCTs) to determine the influence of vitamin D on BMC and fracture risk in children of Black African ancestry are lacking. We conducted a sub-study (n = 450) nested within a phase 3 RCT of weekly oral supplementation with 10 000 IU vitamin D3 vs placebo for 3 yr in HIV-uninfected Cape Town schoolchildren aged 6–11 yr. Outcomes were BMC at the whole body less head (WBLH) and LS and serum 25-hydroxyvitamin D3 (25(OH)D3), PTH, alkaline phosphatase, C-terminal telopeptide, and PINP. Incidence of fractures was a secondary outcome of the main trial (n = 1682). At baseline, mean serum 25(OH)D3 concentration was 70.0 nmol/L (SD 13.5), and 5.8% of participants had serum 25(OH)D3 concentrations &lt;50 nmol/L. Among sub-study participants, end-trial serum 25(OH)D3 concentrations were higher for participants allocated to vitamin D vs placebo (adjusted mean difference [aMD] 39.9 nmol/L, 95% CI, 36.1 to 43.6) and serum PTH concentrations were lower (aMD −0.55 pmol/L, 95% CI, −0.94 to −0.17). However, no interarm differences were seen for WBLH BMC (aMD −8.0 g, 95% CI, −30.7 to 14.7) or LS BMC (aMD −0.3 g, 95% CI, −1.3 to 0.8) or serum concentrations of bone turnover markers. Fractures were rare among participants in the main trial randomized to vitamin D vs placebo (7/755 vs 10/758 attending at least 1 follow-up; adjusted odds ratio 0.70, 95% CI, 0.27 to 1.85). In conclusion, a 3-yr course of weekly oral vitamin D supplementation elevated serum 25(OH)D3 concentrations and suppressed serum PTH concentrations in HIV-uninfected South African schoolchildren of Black African ancestry but did not influence BMC or serum concentrations of bone turnover markers. Fracture incidence was low, limiting power to detect an effect of vitamin D on this outcome.
On the Relationship Between German International Criminal Law and Counter-terrorism Criminal Law
Authors: Geneuss Julia 
Published: January 2024

Abstract
In many cases, and, in particular, in cases concerning crimes committed in the Syrian conflict, an overlap can be identified between international criminal law and counter-terrorism criminal law. The reason for this is the approximative and normative intertwining of these two areas in German criminal law. By way of counter-terrorism criminal law, Germany implemented an organizational crime of membership in an organization whose objective or activities are directed towards the commission of, inter alia, genocide, crimes against humanity, and war crimes, as well as murder. As a consequence, non-state armed groups active in a non-international armed conflict are considered terrorist groups. While this allows for cumulative prosecution, charging, and conviction, in this article an argument will be made that the increasing intertwining of German international criminal law and counter-terrorism criminal law has a problematic side. It blurs the historical, conceptual, and normative differences between the two areas of criminal law. Eventually, this further deepens the asymmetry in the prosecution of state and non-state actors for international crimes.
TGFβ macrophage reprogramming: a new dimension of macrophage plasticity
Authors: Oliver Mary A , Davis Xenia D , Bohannon Julia K 
Published: January 2024

Abstract
The August 2023 article in Science Signaling, “TGF-β uncouples glycolysis and inflammation in macrophages and controls survival during sepsis,” challenges the traditional M1/M2 macrophage classification by investigating the impact of transforming growth factor β on macrophage metabolism and function. Despite its conventional anti-inflammatory role, transforming growth factor β–treated macrophages exhibit a distinct phenotype marked by heightened glycolysis, suppressed proinflammatory cytokines, and increased coagulation factor expression. The study identifies phosphofructokinase, liver type as a crucial glycolytic enzyme regulated by transforming growth factor β via the mTOR–c-MYC pathway. Epigenetic changes induced by transforming growth factor β, such as increased Smad3 activation and reduced proinflammatory transcription factor motif enrichment, contribute to the anti-inflammatory profile. The research extends its implications to sepsis, revealing the role of transforming growth factor β in exacerbating coagulation and reducing survival in mouse models. This effect involves upregulation of coagulation factor F13A1, dependent on phosphofructokinase, liver type activity and glycolysis in macrophages. Connections to COVID-19 pathology are drawn, as transforming growth factor β–treated macrophages and SARS-CoV-2 E protein-exposed cells display similar metabolic profiles. Bioinformatic analysis of COVID-19 patient data suggests correlations between myeloid expression of TGFβR1, PFKL, and F13A1 with disease severity. The study challenges the M1/M2 classification, emphasizing the complexity of macrophage responses influenced by transforming growth factor β, proposing transforming growth factor β as a potential therapeutic target for conditions like sepsis and COVID-19 where dysregulated coagulation is significant. Overall, the research provides valuable insights into transforming growth factor β–mediated immunometabolic regulation, paving the way for future investigations and potential therapeutic interventions.
Integrated Behavioral Health Prevention for Infants in Pediatric Primary Care: A Mixed-Methods Pilot Study
Authors: Ammerman Robert T , Rybak Tiffany M , Herbst Rachel B , Mara Constance A , Zion Cynthia , Patel Meera A , Burstein Emma , Lauer Brea A , Fiat Aria E , Jordan Phoebe , Burkhardt Mary Carol , McClure Jessica M , Stark Lori J 
Published: January 2024

Abstract

Objective
Pediatric primary care is a promising setting in which to deliver preventive behavioral health services to young children and their families. Integrated behavioral health care models typically emphasize treatment rather than prevention. This pilot study examined the efficacy of an integrated behavioral health preventive (IBH-P) intervention delivered by psychologists and focused on supporting parenting in low-income mothers of infants as part of well-child visits in the first 6 months of life.

Methods
Using a mixed-methods approach that included a pilot randomized clinical trial and post-intervention qualitative interviews, 137 mothers were randomly assigned to receive IBH-P or usual care. Self-report measures of parenting, child behavior, and stress were obtained at pre- and/or post-intervention. Direct observation of mother–infant interactions was conducted at post-intervention.

Results
No differences between groups were found on maternal attunement, knowledge of child development, nurturing parenting, or infant behavior. A secondary analysis on a subsample with no prior exposure to IBH-P with older siblings found that mothers in IBH-P reported increased self-efficacy relative to controls. In the qualitative interviews, mothers stated that they valued IBH-P, learning about their baby, liked the integration in primary care, and felt respected and comfortable with their provider.

Conclusions
Findings are discussed in terms of the next steps in refining IBH-P approaches to prevention in primary care.
Pushchino multibeams pulsar search – III. Drift periods of pulsars from summed power spectra method
Authors: Smirnova T V , Tyul’bashev S A , Kitaeva M A , Malofeev V M 
Published: January 2024

ABSTRACT
The drift periods P2 and P3 were searched for using the summed power spectra of 41 pulsars observed at declinations from −9° to +42°. The power spectra of pulses with a given period, pulse width, and drift behaviour have been simulated, the applicability of such a method for estimating drift parameters is shown. For most pulsars, the distribution of harmonic amplitudes in the power spectra corresponds to the expected distribution for these pulsars without drift. At the same time, it was found that for a number of sources, the summed power spectra accumulated over a long period of time give the same drift parameters as those determined by other methods. For 11 pulsars we have defined or redefined the drift period P2. For eight sources the drift period P3 has been determined or redefined. The drift direction of subpulses was redefined for them.
Gas phase ions in protoplanetary discs from collisions of solids
Authors: Penner Jakob , Wurm Gerhard , Teiser Jens 
Published: January 2024

ABSTRACT
Ionization is important for magnetohydrodynamics and chemistry in protoplanetary discs but known ionization sources are often weak along the mid-plane. We present, for the first time, data from a laboratory experiment, where we measure ions from colliding mm-basalt grains emitted into the surrounding gas phase. This positive detection implies that very basic collisions in early phases of planet formation are sources of ionization. The mid-plane of protoplanetary discs might be ionized despite the lack of intense radiation sources.
Elevated HIV Viral Load is Associated with Higher Recombination Rate In Vivo
Authors: Romero Elena V , Feder Alison F 
Published: January 2024

Abstract
HIV’s exceptionally high recombination rate drives its intrahost diversification, enabling immune escape and multidrug resistance within people living with HIV. While we know that HIV’s recombination rate varies by genomic position, we have little understanding of how recombination varies throughout infection or between individuals as a function of the rate of cellular coinfection. We hypothesize that denser intrahost populations may have higher rates of coinfection and therefore recombination. To test this hypothesis, we develop a new approach (recombination analysis via time series linkage decay or RATS-LD) to quantify recombination using autocorrelation of linkage between mutations across time points. We validate RATS-LD on simulated data under short read sequencing conditions and then apply it to longitudinal, high-throughput intrahost viral sequencing data, stratifying populations by viral load (a proxy for density). Among sampled viral populations with the lowest viral loads (&lt;26,800 copies/mL), we estimate a recombination rate of 1.5×10−5 events/bp/generation (95% CI: 7×10−6 to 2.9×10−5), similar to existing estimates. However, among samples with the highest viral loads (&gt;82,000 copies/mL), our median estimate is approximately 6 times higher. In addition to co-varying across individuals, we also find that recombination rate and viral load are associated within single individuals across different time points. Our findings suggest that rather than acting as a constant, uniform force, recombination can vary dynamically and drastically across intrahost viral populations and within them over time. More broadly, we hypothesize that this phenomenon may affect other facultatively asexual populations where spatial co-localization varies.
LINE-1 mRNA 3′ end dynamics shape its biology and retrotransposition potential
Authors: Janecki Damian M , Sen Raneet , Szóstak Natalia , Kajdasz Arkadiusz , Kordyś Martyna , Plawgo Kinga , Pandakov Dmytro , Philips Anna , Warkocki Zbigniew 
Published: January 2024

Abstract
LINE-1 (L1) retrotransposons are mobile genetic elements that create new genomic insertions by a copy-paste mechanism involving L1 RNA/RNP intermediates. L1 encodes two ORFs, of which L1-ORF2p nicks genomic DNA and reverse transcribes L1 mRNA using the nicked DNA as a primer which base-pairs with poly(A) tail of L1 mRNA. To better understand the importance of non-templated L1 3′ ends’ dynamics and the interplay between L1 3′ and 5′ ends, we investigated the effects of genomic knock-outs and temporal knock-downs of XRN1, DCP2, and other factors. We hypothesized that in the absence of XRN1, the major 5′→3′ exoribonuclease, there would be more L1 mRNA and retrotransposition. Conversely, we observed that loss of XRN1 decreased L1 retrotransposition. This occurred despite slight stabilization of L1 mRNA, but with decreased L1 RNP formation. Similarly, loss of DCP2, the catalytic subunit of the decapping complex, lowered retrotransposition despite increased steady-state levels of L1 proteins. In both XRN1 and DCP2 depletions we observed shortening of L1 3′ poly(A) tails and their increased uridylation by TUT4/7. We explain the observed reduction of L1 retrotransposition by the changed qualities of non-templated L1 mRNA 3′ ends demonstrating the important role of L1 3′ end dynamics in L1 biology.
Minimization of the E. coli ribosome, aided and optimized by community science
Authors: Tangpradabkul Tiyaporn , Palo Michael , Townley Jill , Hsu Kenneth B , participants Eterna , Smaga Sarah , Das Rhiju , Schepartz Alanna 
Published: January 2024

Abstract
The ribosome is a ribonucleoprotein complex found in all domains of life. Its role is to catalyze protein synthesis, the messenger RNA (mRNA)-templated formation of amide bonds between α-amino acid monomers. Amide bond formation occurs within a highly conserved region of the large ribosomal subunit known as the peptidyl transferase center (PTC). Here we describe the step-wise design and characterization of mini-PTC 1.1, a 284-nucleotide RNA that recapitulates many essential features of the Escherichia coli PTC. Mini-PTC 1.1 folds into a PTC-like structure under physiological conditions, even in the absence of r-proteins, and engages small molecule analogs of A- and P-site tRNAs. The sequence of mini-PTC 1.1 differs from the wild type E. coli ribosome at 12 nucleotides that were installed by a cohort of citizen scientists using the on-line video game Eterna. These base changes improve both the secondary structure and tertiary folding of mini-PTC 1.1 as well as its ability to bind small molecule substrate analogs. Here, the combined input from Eterna citizen-scientists and RNA structural analysis provides a robust workflow for the design of a minimal PTC that recapitulates many features of an intact ribosome.
The Making of Corporate Legal Concession Theory
Authors: Hardman Jonathan 
Published: January 2024

Abstract
Professor Watson’s The Making of the Modern Company traces the development of the modern corporate form back to the East India Company, disproving a common notion that company law originated solely with small, private companies. This review article argues three key implications of this excellent book. First, Watson focuses on the duality of the modern company—with state-provided and private features. This cuts through, and goes a long way to resolving, the ongoing historic debate as to the nature of the company. Second, the primary unit of study chosen—the modern company—reminds corporate lawyers of our role in studying this duality in a very crowded field. Third, despite eschewing ‘concession theories’ of company law (which hold that the company is merely a concession from the state), Watson demonstrates a role for the state in the modern company that is often overlooked.
Sequential Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor-Induced Radical Surgery in Oligometastatic Non–Small Cell Lung Cancer: A Case Report
Authors: Wang Huaiyu , Fan Zaiwen , Yang Xiaoming , Wu Qing , Jiang Suxin , Zhu Jingna , Liu Jie , Zhou Chuanhong , Liu Yinghui , You Xia , Han Yong 
Published: January 2024

Abstract
Sequential regimens in patients with epidermal growth factor receptor (EGFR) mutation-positive non–small cell lung cancer (NSCLC) can overcome tyrosine kinase inhibitor (TKI) resistance and maximize clinical benefit. Patients with advanced NSCLC can achieve excellent tumor control after a period of EGFR-TKI treatment. Patients may benefit from additional local treatment, such as surgery or radiation therapy, once the tumor is under control. Here, we present a case of a patient with advanced oligometastatic NSCLC with EGFR mutations who achieved downstaging through sequential EGFR-TKI-based precision medicine allowing resection of residual disease.
Upland Sandpipers select for later time since fire and experience high nest survival in grasslands managed with patch-burn grazing
Authors: Rischette Alexander C , Geaumont Benjamin A , Duquette Cameron A , Hovick Torre J 
Published: January 2024

Abstract
Upland Sandpipers (Bartramia longicauda) are a grassland obligate shorebird that nests in dense vegetation structure near recently disturbed areas and could benefit from management practices that promote heterogenous vegetation structure. Upland Sandpipers primary breeding range is generally managed for livestock production using traditional practices that lack patchy disturbances to facilitate higher levels of structural heterogeneity. Patch-burn grazing (PBG) could be an alternative management practice for Upland Sandpiper conservation for its use to create areas of dense vegetation structure near recently disturbed areas. However, limited information is available regarding nest production of Upland Sandpipers within a PBG framework. To assess the compatibility of PBG with Upland Sandpiper conservation, we estimated nest site selection and survival of Upland Sandpiper nests on private lands managed with PBG in the unglaciated plains region of North Dakota. We located 59 nests from 2017 to 2020. Upland Sandpipers avoided 1 year since fire (YSF) patches and selected for 2 and 3 YSF patches for nest sites. Additionally, nest site selection decreased with increased bare ground and at intermediate distances to the nearest Upland Sandpiper nest. Upland Sandpipers experienced high overall nest survival during the study with 51 of 59 nests successfully hatching, which limited our ability to make inferences between daily survival rates and variables of interest. Our findings suggest that PBG can provide suitable nesting cover for Upland Sandpipers in later YSF patches despite annual prescribed fire and livestock grazing during the nesting season. PBG seems a suitable grassland management strategy that should be included in conservation planning within Upland Sandpiper’s breeding distribution.