bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic profile in plasma as a biomarker of pregnancy in cows
Authors: Mojsym Wioleta , Wawrzykowski Jacek , Kankofer Marta 
Published: July 2024

AbstractPregnancy has its own protein dynamics, reflecting the hormonal profile. Quantitative and qualitative changes in plasma protein profile may provide useful information about this condition. Any alterations may be a signal heralding clinical or subclinical pathology. The objective of our study was to compare the plasma protein profile between selected months of pregnancy in cows for a better understanding gestation course. For this purpose, we collected blood from healthy pregnant (n = 30; n = 6 for each pregnancy stage) and non‐pregnant (C; n = 6) Holstein‐Friesian cows during a routine veterinary examination. Collected samples were selected according to pregnancy month (first, second, third, sixth, and ninth), prepared, and separated by two‐dimensional electrophoresis. The Delta‐2D program compared and statistically evaluated scanned gel images from the appropriate months. The mean volume of the spots was considered. The MALDI TOF/TOF spectrometer was used to identify statistically significant proteins. There were 11 distinct proteins found, including peptidyl‐prolyl cis‐trans isomerase F, oligoribonuclease, and PRELI domain‐containing protein 3B (all of them have the lowest abundance in the C group), alpha‐1B‐glycoprotein, L‐gulonolactone oxidase, hemopexin (first month with higher abundance than control), alpha‐2‐HS‐glycoprotein (significantly higher abundance in the first month than in remaining groups), ermin (absent in the first month and lower abundance in the third and sixth months than in the remaining groups and control), endophilin‐A2 (significant differences between the control and the second, third, sixth, and ninth months), apolipoprotein A‐I (significant difference between control and the first and sixth months), alpha‐1‐antiproteinase (significant difference between control and the ninth month). The study demonstrated the distinctions between plasma protein composition and alterations during the pregnancy course which may potentially serve as diagnostic tools.
Principles of an economic sociology of innovation
Authors: Reale Filippo 
Published: July 2024

AbstractAlthough innovation is a core element of capitalist dynamics, it turns out that, to date, there is no coherent Economic Sociology of innovation, leaving the discipline oblivious to explaining fundamental economic dynamics. Nor has the enormous importance of novelty and innovation in current societal transitions evoked a corresponding research program in Economic Sociology, meaning that Economic Sociology struggles to grasp contemporary societal change. The article reviews the rather disparate diversity of approaches that could speak to a remedy, stepwise assembling and integrating them to establish the principles of an Economic Sociology approach to innovation. First, resonating with ‘embeddedness’ as the core paradigm of Economic Sociology, it spells out the embeddedness of innovation processes in social institutions. Next, it reviews innovation in relation to the diversity of normative, cultural‐cognitive, regulative, and relational institutions, carving out the relevance of the combination of institutions in ‘fields.’ It then determines ‘valuation’ as the overarching mechanism of how institutional frameworks interact with innovation processes. Eventually, discussing ‘institutional work’ as a major property of institutional frameworks, it raises awareness for the mechanisms of the ‘co‐evolution’ of institutions and innovations.
Measuring cultural identities in cultural theory survey research
Authors: Johnson Branden B. , Swedlow Brendon 
Published: July 2024

AbstractObjectiveEfforts to measure cultural identities in survey research rely on self‐reported ethnic, racial, and national identities. We test how survey operationalization of grid–group cultural theory (CT) influences the classification of individuals’ (sub)cultural identities.MethodsA national online sample of Americans (n = 697 for current analyses) rated items from CT indices, CT statements, and cultural cognition theory (CCT) indices in a 2016–2017 panel survey. Individuals were classified as identifying with a culture if they supported it (e.g., rating it above the scale mean or median, or in the top 35 percent of the scale distribution) or agreed with each item constituting the scale (the “midpoint method” introduced here).ResultsDifferent classification methods and cultural measures yield different proportions of support of cultural biases, yielding statistically significant differences despite most people being similarly classified. Survey measures can unequivocally assign a minority of people to a single cultural identity, with a majority so classified only if one does not require the individual to support only one bias.ConclusionsUsing a short, conceptually valid measure of culture with the novel midpoint method seems best for CT survey researchers but should have implications more broadly in cultural identity research and social science efforts to classify individuals.
PaMYB11 promotes suberin deposition in Norway spruce embryogenic tissue during cryopreservation: A novel resistance mechanism against osmosis
Authors: Hu Jiwen , Zhu Tianqing , Yao Chengcheng , Hao Chunhui , Yan Huiling , Pu Ziyan , Ma Wenjun , Gao Benwang , Gao Han , Kong Lisheng , Zhang Hanguo , Wang Junhui 
Published: July 2024

SUMMARYThe osmotic resistance mechanism has been extensively studied in whole plants or plant tissues. However, little is known about it in embryogenic tissue (ET) which is widely used in plant‐based biotechnological systems. Suberin, a cell wall aliphatic and aromatic heteropolymer, plays a critical role in plant cells against osmosis stress. The suberin regulatory biosynthesis has rarely been studied in gymnosperms. Here, PaMYB11, a subgroup 11 R2R3‐MYB transcription factor, plays a key role in the osmotic resistance of Norway spruce (Picea abies) ETs during cryoprotectant pretreatment. Thus, RNA‐seq, histological, and analytical chemical analyses are performed on the stable transformations of PaMYB11‐OE and PaMYB11‐SRDX in Norway spruce ETs. DAP‐seq, Y1H, and LUC are further combined to explore the PaMYB11 targets. Activation of PaMYB11 is necessary and sufficient for suberin lamellae deposition on Norway spruce embryogenic cell walls, which plays a decisive role in ET survival under osmotic stress. Transcriptome analysis shows that PaMYB11 enhances suberin lamellae monomer synthesis by promoting very long‐chain fatty acid (VLCFA) synthesis. PaPOP, PaADH1, and PaTET8L, the first two (PaADH1 and PaPOP, included) involved in VLCFA synthesis, are proved to be the direct targets of PaMYB11. Our study identified a novel osmotic response directed by PaMYB11 in Norway spruce ET, which provides a new understanding of the resistance mechanism against osmosis in gymnosperms.
Intersection matrices for the minimal regular model of X0(N)${X}_0(N)$ and applications to the Arakelov canonical sheaf
Authors: Dolce Paolo , Mercuri Pietro 
Published: July 2024

AbstractLet be an integer coprime to 6 such that and let be the genus of the modular curve . We compute the intersection matrices relative to special fibres of the minimal regular model of . Moreover, we prove that the self‐intersection of the Arakelov canonical sheaf of is asymptotic to , for .
Zafirlukast induces DNA condensation and has bactericidal effect on replicating
Mycobacterium abscessus
Authors: Niet Sanne van der , Green Keith D. , Schimmel Irene M. , Bakker Jordy de , Lodder Bastiaan , Reits Eric A. , Garneau-Tsodikova Sylvie , van der Wel Nicole N. 
Published: July 2024

ABSTRACT

Mycobacterium abscessus
infections are emerging in cystic fibrosis patients, and treatment success rate in these patients is only 33% due to extreme antibiotic resistance. Thus, new treatment options are essential. An interesting target could be Lsr2, a nucleoid-associated protein involved in mycobacterial virulence. Zafirlukast is a Food and Drug Administration (FDA)-approved drug against asthma that was shown to bind Lsr2. In this study, zafirlukast treatment is shown to reduce
M. abscessus
growth, with a minimal inhibitory concentration of 16 µM and a bactericidal concentration of 64 µM in replicating bacteria only. As an initial response, DNA condensation, a known stress response of mycobacteria, occurs after 1 h of treatment with zafirlukast. During continued zafirlukast treatment, the morphology of the bacteria alters and the structural integrity of the bacteria is lost. After 4 days of treatment, reduced viability is measured in different culture media, and growth of
M. abscessus
is reduced in a dose-dependent manner. Using transmission electron microscopy, we demonstrated that the hydrophobic multilayered cell wall and periplasm are disorganized and ribosomes are reduced in size and relocalized. In summary, our data demonstrate that zafirlukast alters the morphology of
M. abscessus
and is bactericidal at 64 µM. The bactericidal concentration of zafirlukast is relatively high, and it is only effective on replicating bacteria but as zafirlukast is an FDA-approved drug, and currently used as an anti-asthma treatment, it could be an interesting drug to further study in
in vivo
experiments to determine whether it could be used as an antibiotic for
M. abscessus
infections.
Pharmacokinetics and safety of GST-HG171, a novel 3CL protease inhibitor, in Chinese subjects with impaired and normal liver function
Authors: Zhou Jing , Zhang Hong , Chen Hong , Zhang George , Mao John , Zhang Tianxiang , Tang Yanan , Yan Wenhao , Li Chuanjing , Ding Yanhua , Jin Qinglong 
Published: July 2024

ABSTRACT

GST-HG171 is a potent, broad-spectrum, orally bioavailable small-molecule 3C-like (3CL) protease inhibitor that was recently approved for treating mild to moderate coronavirus disease 2019 patients in China. Since cytochrome P450 (CYP) enzymes, primarily CYP3A, are the main metabolic enzymes of GST-HG171, hepatic impairment may affect its pharmacokinetic (PK) profile. Aiming to guide clinical dosing for patients with hepatic impairment, this study, using a non-randomized, open-label, single-dose design, assessed the impact of hepatic impairment on the PK, safety, and tolerability of GST-HG171. Patients with mild and moderate hepatic impairment along with healthy subjects were enrolled (
n
= 8 each), receiving a single oral dose of 150 mg GST-HG171, with concurrent administration of 100 mg ritonavir to sustain CYP3A inhibition before and after GST-HG171 administration (−12, 0, 12, and 24 hours). Compared to subjects with normal hepatic function, the geometric least-squares mean ratios (90% confidence intervals) for GST-HG171’s maximum plasma concentration (
C
max
), area under the concentration-time curve up to the last quantifiable time (AUC

0-
t

), and area under the plasma concentration-time curve from time 0 extrapolated to infinity (AUC
0-∞
) in subjects with mild hepatic impairment were 1.14 (0.99, 1.31), 1.07 (0.88, 1.30), and 1.07 (0.88, 1.29), respectively. For moderate hepatic impairment, the ratios were 0.87 (0.70, 1.07), 0.82 (0.61, 1.10), and 0.82 (0.61, 1.10), respectively. Hepatic impairment did not significantly alter GST-HG171’s peak time (
T
max
) and elimination half-life (
T
1/2
). GST-HG171 exhibited good safety and tolerability in the study. Taken together, mild to moderate hepatic impairment minimally impacted GST-HG171 exposure, suggesting no need to adjust GST-HG171 dosage for patients with mild to moderate hepatic impairment in the clinic.

Clinical Trials

Registered at ClinicalTrials.gov (
NCT06106113
).
An optimized cyclophosphamide-treated mouse model of
Mycobacterium abscessus
pulmonary infection
Authors: Sun Yan , Zhang Kaixi , Delos Santos May , Pee Carmen J. E. , Yang Yanmeng , Kang Meiqi , Shin Sung Jae , Chan-Park Mary B. , Pethe Kevin 
Published: July 2024

ABSTRACT

Mycobacterium abscessus
pulmonary infections are increasingly problematic, especially for immunocompromised individuals and those with underlying lung conditions. Currently, there is no reliable standardized treatment, underscoring the need for improved preclinical drug testing. We present a simplified immunosuppressed mouse model using only four injections of cyclophosphamide, which allows for sustained
M. abscessus
lung burden for up to 16 days. This model proved effective for antibiotic efficacy evaluation, as demonstrated with imipenem or amikacin.
Substitutions in the nonactive site of the passenger domain on the activity of
Haemophilus influenzae
immunoglobulin A1 protease
Authors: Chen Chi-Wei , Ho Cheng-Hsun 
Published: July 2024

ABSTRACT

Immunoglobulin A1 (IgA1) protease is a critical virulence factor of
Haemophilus influenzae
that facilitates bacterial mucosal infection. This study investigates the effect of
iga
gene polymorphism on the enzymatic activity of
H. influenzae
IgA1 protease. The IgA1 protease activity was examined in the
H. influenzae
Rd KW20 strain and 51 isolates. Genetic variations in
iga
and deduced amino acid substitutions affecting IgA1 protease activity were assessed. Machine learning tools and functional complementation assays were used to analyze the effects of identified substitutions on the stability and activity of IgA1 protease, respectively. All 51 isolates exhibited similar
iga
expression levels. No
igaB
expression was detected. According to comparisons with the reference Rd KW20 strain, four substitutions in the protease domain, 26 in the nonprotease passenger domain, and two in the β-barrel domain were associated with the change in IgA1 protease activity. No substitutions in the catalytic site of IgA1 protease were observed. Logistic regression, receiver operating characteristic curves, Venn diagrams, and protein stability analyses revealed that the substitutions Asn352Lys, Pro353Ala, Lys356Asn, Gln916Lys, and Gly917Ser, which were located in the nonactive site of the passenger domain, were associated with decreases in IgA1 protease activity and stability, whereas Asn914Lys was associated with an increase in these events. Functional complementation assays revealed that the Asn914Lys substitution increased IgA1 protease activity in the Rd KW20 strain. This study identified substitutions in the nonactive site of the passenger domain that affect both the activity and stability of
H. influenzae
IgA1 protease.
Divergent effects of
emm
types 1 and 12 on invasive group A streptococcal infections—results of a retrospective cohort study, Germany 2023
Authors: Bertram Ralph , Itzek Andreas , Marr Lisa , Manzke Jana , Voigt Sebastian , Chapot Valérie , van der Linden Mark , Rath Peter-Michael , Hitzl Wolfgang , Steinmann Joerg 
Published: July 2024

ABSTRACT

As a potential side effect of the severe acute respiratory syndrome coronavirus type 2 pandemic, invasive group A
Streptococcus
(iGAS) infections in Europe have increased dramatically in both children and adults in the end of 2022. This epidemiological and molecular study describes the distributions of streptococcal genes encoding the M antigen (
emm
types) and superantigens in patients with invasive and non-invasive GAS infections. From December 2022 to December 2023, a total of 163 GAS isolates were collected from sterile and non-sterile sites of patients at five hospitals in Germany including two tertiary care centers. Genes encoding M protein and superantigens were determined following the guidelines of CDC Streptococcus laboratory. Patients’ characteristics were reviewed retrospectively. Correlations of clinical factors,
emm
types, and superantigens with rates of invasive infections were analyzed. Of the 163 included GAS cases, 112 (69%) were considered as invasive. In total, 33 different
emm
types were observed, of which
emm1.0
(
n
= 49; 30%),
emm89.0
(
n
= 15; 9%), and
emm12.0
(
n
= 14; 9%) were most prevalent. In total, 70% of
emm1.0
isolates belonged to M1
UK
lineage. No difference in invasive infections was observed for the M1
UK
lineage compared with other
emm1.0
isolates. However, the
emm1.0
type, presence of
speA1-3
,
speG
, or
speJ
, as well as adulthood were significantly associated with invasive infections. In contrast,
emm12.0
isolates were significantly less associated with invasive infections. Multivariable analysis confirmed a significant influence of
speJ
and adulthood on iGAS infections. This study underlines the importance of continuous monitoring of genomic trends and identification of emerging GAS variants. This may aid in delineating pathogenicity factors of
Streptococcus pyogenes
that propel invasive infections.
Variability in
n
-caprylate and
n
-caproate producing microbiomes in reactors with in-line product extraction
Authors: Spirito Catherine M. , Lucas Timo N. , Patz Sascha , Jeon Byoung Seung , Werner Jeffrey J. , Trondsen Lauren H. , Guzman Juan J. , Huson Daniel H. , Angenent Largus T. 
Published: July 2024

ABSTRACT

Medium-chain carboxylates (MCCs) are used in various industrial applications. These chemicals are typically extracted from palm oil, which is deemed not sustainable. Recent research has focused on microbial chain elongation using reactors to produce MCCs, such as
n
-caproate (C6) and
n
-caprylate (C8), from organic substrates such as wastes. Even though the production of
n
-caproate is relatively well-characterized, bacteria and metabolic pathways that are responsible for
n
-caprylate production are not. Here, three 5 L reactors with continuous membrane-based liquid-liquid extraction (i.e., pertraction) were fed ethanol and acetate and operated for an operating period of 234 days with different operating conditions. Metagenomic and metaproteomic analyses were employed.
n
-Caprylate production rates and reactor microbiomes differed between reactors even when operated similarly due to differences in H
2
and O
2
between the reactors. The complete reverse β-oxidation (RBOX) pathway was present and expressed by several bacterial species in the
Clostridia
class. Several
Oscillibacter
spp., including
Oscillibacter valericigenes
, were positively correlated with
n
-caprylate production rates, while
Clostridium kluyveri
was positively correlated with
n
-caproate production.
Pseudoclavibacter caeni
, which is a strictly aerobic bacterium, was abundant across all the operating periods, regardless of
n
-caprylate production rates. This study provides insight into microbiota that are associated with
n
-caprylate production in open-culture reactors and provides ideas for further work.

IMPORTANCE

Microbial chain elongation pathways in open-culture biotechnology systems can be utilized to convert organic waste and industrial side streams into valuable industrial chemicals. Here, we investigated the microbiota and metabolic pathways that produce medium-chain carboxylates (MCCs), including
n
-caproate (C6) and
n
-caprylate (C8), in reactors with in-line product extraction. Although the reactors in this study were operated similarly, different microbial communities dominated and were responsible for chain elongation. We found that different microbiota were responsible for
n
-caproate or
n
-caprylate production, and this can inform engineers on how to operate the systems better. We also observed which changes in operating conditions steered the production toward and away from
n
-caprylate, but more work is necessary to ascertain a mechanistic understanding that could be predictive. This study provides pertinent research questions for future work.
A translithospheric magmatic system revealed beneath Changbaishan volcano
Authors: Zhang Zhou , Deng Yangfan , Xu Yi-Gang , Li Xin 
Published: July 2024

Abstract
Changbaishan volcano (CBV), located on the border between China and North Korea, has undergone violent eruptions since the Oligocene, making it one of the most captivating and explosive volcanoes on Earth. However, the lack of precise characterization regarding the magmatic system makes it difficult to decipher its eruption risk and mechanism, despite its significant size and past devastating effects. In this study, we employed newly developed teleseismic receiver function techniques, including Ps and Sp waves, to construct a lithospheric structure model beneath the CBV region. The results show a thick crust (~37 km) and a weak, thin lithosphere under the CBV, with a low-amplitude width of 80 km at the Moho depth and 200 km at the depth of the lithosphere-asthenosphere boundary. These features depict the seismological response of a translithospheric magmatic system beneath the CBV, where hot upwelling material rises through the lithospheric mantle, underplates at the base of the crust, and forms the magma chamber(s) at shallow depth. Such magmatic system features can be taken as a unifying paradigm for large volcanic regions worldwide.
How feasible or useful are timeliness metrics as a tool to optimise One Health outbreak responses?
Authors: Fieldhouse Jane , Nakiire Lydia , Kayiwa Joshua , Brindis Claire D , Mitchell Ashley , Makumbi Issa , Ario Alex Riolexus , Fair Elizabeth , Mazet Jonna A K , Lamorde Mohammed 
Published: July 2024

IntroductionAs timeliness metrics gain traction to assess and optimise outbreak detection and response performance, implementation and scale-up require insight into the perspectives of stakeholders adopting these tools. This study sought to characterise the feasibility and utility of tracking One Health outbreak milestones across relevant human, animal, plant, and environmental sectors to systematically quantify timeliness metrics in Uganda, a country prone to outbreaks of WHO priority diseases.MethodsA database of outbreak events occurring in Uganda between 2018 and 2022 was compiled. Outbreak reports meeting our inclusion criteria were reviewed to quantify the frequency of milestone reporting. Key informant interviews were conducted with expert stakeholders to explore the feasibility and utility of tracking metrics using a framework analysis. Quantitative and qualitative data were collected and analysed concurrently.ResultsOf the 282 public health emergencies occurring between 2018 and 2022, 129 events met our inclusion criteria, and complete data were available for 82 outbreaks. For our qualitative portion, 10 informants were interviewed from 7 institutions, representing the human, animal and environmental sectors. Informants agreed most One Health milestones are feasible to track, which was supported by the frequency of milestone reporting; however, there was a demonstrated need for increased reporting of after-action reviews, as well as outbreak start and end dates. Predictive alerts signalling potential outbreaks and preventive responses to alerts are seen as challenging to routinely capture, reflecting the lack of public health action for these domains.ConclusionDespite consensus among stakeholders that timeliness metrics are a beneficial tool to assess outbreak performance, not all One Health metrics are being tracked consistently, thereby missing opportunities to optimise epidemic intelligence, preparedness and prevention. The feasibility of tracking these metrics depends on the integration of reporting channels, enhanced documentation of milestones and development of guidance for early adopters, recognising country-specific on-the-ground realities and challenges to national scaling efforts.