bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of environmental factors on low temperature anaerobic digestion of pig manure
Authors: Yang Bin , Wang Changmei , Zhao Xingling , Liu Jianfeng , Yin Fang , Liang Chengyue , Wu Kai , Liu Jing , Yang Hong , Zhang Wudi 
Published: November 2022

Abstract
In this study, we investigated the inhibitory effect of low temperature on biogas fermentation system. Biogas fermentation inoculum was domesticated at 4 °C, and subsequently inoculated into pig manure feedstock in a batch biogas fermentation process. A low-temperature biogas fermentation system was maintained at 9 °C, and its abiotic factors, bacterial community, and archaeal community were determined. The results showed that (1) the biogas fermentation lasted for 160 days, with a total gas production of 19,150 ml, including N2 production of 11,370 ml, CO2 production of 3,534 ml, and CH4 production of 3,031 ml. (2) The average relative abundance of the primary dominant bacterium operational taxonomic unit (OTU) was 30%, with 100% similarity to
Pseudomonas caeni
, atypical denitrifying bacterium. The average relative abundance of the secondary dominant bacterium OTU was 20.36%, with 99% similarity to
Clostridium cellulovorans,
a typical cellulose- and hemicellulose-degrading bacterium. The average relative abundance of the primary dominant methanogenic archaeon OTU was 7.22%, with 99% similarity to Methanosphaera cuniculi, a typical methylotrophic methanogen, and the secondary dominant methanogenic archaeon OTU had an average relative abundance of 4.15%, with 98% similarity to Methanocorpusculum sinense, a typical hydrogenotrophic methanogen. (3) The primary dominant bacterial genus Pseudomonas exhibited highly significant negative correlations with the dominant biogas-producing microorganisms such as Clostridium, Terrisporobacter, Turicibacter, Methanosphaera, and Methanocorpusculum. We concluded that (1) high concentrations of abiotic factors such as ammonia nitrogen, acetic acid, and propionic acid were important indicators of relatively poor operation of low-temperature biogas fermentation systems, while (2) high numbers of MCG archaea and Pseudomonas were important biotic factors showing comparatively poor operation of the system.
Assessment and prediction of glioblastoma therapy response: challenges and opportunities
Authors: Qi Dan , Li Jing , Quarles C Chad , Fonkem Ekokobe , Wu Erxi 
Published: November 2022

AbstractGlioblastoma is the most aggressive type of primary adult brain tumour. The median survival of patients with glioblastoma remains approximately 15 months, and the 5-year survival rate is &lt;10%. Current treatment options are limited, and the standard of care has remained relatively constant since 2011. Over the last decade, a range of different treatment regimens have been investigated with very limited success. Tumour recurrence is almost inevitable with the current treatment strategies, as glioblastoma tumours are highly heterogeneous and invasive. Additionally, another challenging issue facing patients with glioblastoma is how to distinguish between tumour progression and treatment effects, especially when relying on routine diagnostic imaging techniques in the clinic. The specificity of routine imaging for identifying tumour progression early or in a timely manner is poor due to the appearance similarity of post-treatment effects. Here, we concisely describe the current status and challenges in the assessment and early prediction of therapy response and the early detection of tumour progression or recurrence. We also summarize and discuss studies of advanced approaches such as quantitative imaging, liquid biomarker discovery and machine intelligence that hold exceptional potential to aid in the therapy monitoring of this malignancy and early prediction of therapy response, which may decisively transform the conventional detection methods in the era of precision medicine.
LitCovid ensemble learning for COVID-19 multi-label classification
Authors: Gu Jinghang , Chersoni Emmanuele , Wang Xing , Huang Chu-Ren , Qian Longhua , Zhou Guodong 
Published: November 2022

AbstractThe Coronavirus Disease 2019 (COVID-19) pandemic has shifted the focus of research worldwide, and more than 10 000 new articles per month have concentrated on COVID-19–related topics. Considering this rapidly growing literature, the efficient and precise extraction of the main topics of COVID-19–relevant articles is of great importance. The manual curation of this information for biomedical literature is labor-intensive and time-consuming, and as such the procedure is insufficient and difficult to maintain. In response to these complications, the BioCreative VII community has proposed a challenging task, LitCovid Track, calling for a global effort to automatically extract semantic topics for COVID-19 literature. This article describes our work on the BioCreative VII LitCovid Track. We proposed the LitCovid Ensemble Learning (LCEL) method for the tasks and integrated multiple biomedical pretrained models to address the COVID-19 multi-label classification problem. Specifically, seven different transformer-based pretrained models were ensembled for the initialization and fine-tuning processes independently. To enhance the representation abilities of the deep neural models, diverse additional biomedical knowledge was utilized to facilitate the fruitfulness of the semantic expressions. Simple yet effective data augmentation was also leveraged to address the learning deficiency during the training phase. In addition, given the imbalanced label distribution of the challenging task, a novel asymmetric loss function was applied to the LCEL model, which explicitly adjusted the negative–positive importance by assigning different exponential decay factors and helped the model focus on the positive samples. After the training phase, an ensemble bagging strategy was adopted to merge the outputs from each model for final predictions. The experimental results show the effectiveness of our proposed approach, as LCEL obtains the state-of-the-art performance on the LitCovid dataset.Database URL: https://github.com/JHnlp/LCEL
Cardiac involvement in non-cirrhotic portal hypertension: MRI detects myocardial fibrosis and oedema similar to compensated cirrhosis
Authors: Isaak Alexander , Chang Johannes , Mesropyan Narine , Kravchenko Dmitrij , Endler Christoph , Bischoff Leon , Böhling Nina , Pieper Claus C , Kuetting Daniel , Strassburg Christian P , Attenberger Ulrike , Jansen Christian , Praktiknjo Michael , Luetkens Julian A 
Published: November 2022

Abstract

Aims
The exact role of portal hypertension in cirrhotic cardiomyopathy remains unclear, and it is uncertain whether cardiac abnormalities also occur in non-cirrhotic portal hypertension (NCPH). This magnetic resonance imaging (MRI) study aimed to evaluate the presence of subclinical myocardial dysfunction, oedema, and fibrosis in NCPH.

Methods and results
In this prospective study (2018–2022), participants underwent multiparametric abdominal and cardiac MRI including assessment of cardiac function, myocardial oedema, late gadolinium enhancement (LGE), and abdominal and cardiac mapping [T1 and T2 relaxation times, extracellular volume fraction (ECV)]. A total of 111 participants were included [44 participants with NCPH (48 ± 15 years; 23 women), 47 cirrhotic controls, and 20 healthy controls]. The cirrhotic group was dichotomized (Child A vs. Child B/C). NCPH participants demonstrated a more hyperdynamic circulation compared with healthy controls (cardiac index: 3.7 ± 0.6 vs. 3.2 ± 0.8 L/min/m², P = 0.004; global longitudinal strain: −27.3 ± 4.6 vs. −24.6 ± 3.5%, P = 0.022). The extent of abnormalities indicating myocardial fibrosis and oedema in NCPH was comparable with Child A cirrhosis (e.g. LGE presence: 32 vs. 33 vs. 69%, P = 0.004; combined T1 and T2 elevations: 46 vs. 27 vs. 69%, P = 0.017; NCPH vs. Child A vs. Child B/C). Correlations between splenic T1 and myocardial T1 values were found (r = 0.41; P = 0.007). Splenic T1 values were associated with the presence of LGE (odds ratio, 1.010; 95% CI: 1.002, 1.019; P = 0.013).

Conclusion
MRI parameters of myocardial fibrosis and oedema were altered in participants with NCPH to a similar extent as in compensated cirrhosis and were associated with splenic markers of portal hypertension, indicating specific portal hypertensive cardiomyopathy.
International Trade and Innovation Dynamics with Endogenous Markups
Authors: Cavenaile Laurent , Roldan-Blanco Pau , Schmitz Tom 
Published: November 2022

Abstract
We argue that the recent increases in market concentration and markups are partly due to an ‘innovation feedback effect’ of globalisation. Lower trade costs increase innovation incentives for global firms. As the winners of the ensuing innovation race increase their technological advantage, concentration and markups rise. We develop an endogenous growth model capturing this effect and calibrate it to US manufacturing data. We find that the increase in trade between 1989 and 2007 raised the aggregate markup by 3.5 percentage points. This is entirely due to innovation: without the innovation response, markups would have fallen by 4 percentage points.
Transposable Elements Continuously Remodel the Regulatory Landscape, Transcriptome, and Function of Decidual Stromal Cells
Authors: Mika Katelyn , Lynch Vincent J 
Published: November 2022

AbstractGene expression evolution underlies the origin, divergence, and conservation of biological characters including cell-types, tissues, and organ systems. Previously we showed that large-scale gene expression changes in decidual stromal cells (DSCs) contributed to the origins of pregnancy in eutherians and the divergence of pregnancy traits in primates and that transposable elements likely contributed to these gene expression changes. Here we show that two large waves of TEs remodeled the transcriptome and regulatory landscape of DSCs, including a major wave in primates. Genes nearby TE-derived regulatory elements are among the most progesterone responsive in the genome and play essential roles in orchestrating progesterone responsiveness and the core function of decidual cells by donating progesterone receptor binding sites to the genome. We tested the regulatory abilities of 89 TE consensus sequences and found that nearly all of them acted as repressors in mammalian cells, but treatment with a histone deacetylase inhibitor unmasked latent enhancer functions. These data indicate that TEs have played an important role in the development, evolution, and function of primate DSCs and suggest a two-step model in which latent enhancer functions of TEs are unmasked after they lose primary repressor functions.
Liposomal amphotericin B—the future
Authors: Hoenigl M , Lewis R , van de Veerdonk F L , Verweij P E , Cornely O A 
Published: November 2022

AbstractAdvances in medicine have led to a growing number of people with compromised or suppressed immune systems who are susceptible to invasive fungal infections. In particular, severe fungal infections are becoming increasingly common in ICUs, affecting people within and outside of traditional risk groups alike. This is exemplified by the emergence of severe viral pneumonia as a significant risk factor for invasive pulmonary aspergillosis, and the recognition of influenza-associated pulmonary aspergillosis and, more recently, COVID-19-associated pulmonary aspergillosis.The treatment landscape for haematological malignancies has changed considerably in recent years, and some recently introduced targeted agents, such as ibrutinib, are increasing the risk of invasive fungal infections. Consideration must also be given to the risk of drug–drug interactions between mould-active azoles and small-molecule kinase inhibitors.At the same time, infections caused by rare moulds and yeasts are increasing, and diagnosis continues to be challenging. There is growing concern about azole resistance among both moulds and yeasts, mandating continuous surveillance and personalized treatment strategies.It is anticipated that the epidemiology of fungal infections will continue to change and that new populations will be at risk. Early diagnosis and appropriate treatment remain the most important predictors of survival, and broad-spectrum antifungal agents will become increasingly important. Liposomal amphotericin B will remain an essential therapeutic agent in the armamentarium needed to manage future challenges, given its broad antifungal spectrum, low level of acquired resistance and limited potential for drug–drug interactions.
Pharmacokinetics and soft-tissue distribution of tebipenem pivoxil hydrobromide using microdialysis: a study in healthy subjects and patients with diabetic foot infections
Authors: Abouelhassan Yasmeen , Fratoni Andrew J , Shepard Ashley K , Nicolau David P , Asempa Tomefa E 
Published: November 2022

Abstract

Objective
Tebipenem pivoxil hydrobromide is a novel oral carbapenem prodrug of tebipenem, the active moiety. We assessed tebipenem steady-state pharmacokinetics in the skin and soft tissue in healthy subjects and infected patients with diabetes using in vivo microdialysis.

Methods
Six healthy subjects and six patients with an ongoing diabetic foot infection (DFI) received tebipenem pivoxil hydrobromide 600 mg orally every 8 h for three doses. A microdialysis probe was inserted in the thigh of healthy subjects or by the wound margin in patients. Plasma and dialysate samples were obtained immediately prior to the third dose and sampled over 8 h.

Results
Tebipenem plasma protein binding (mean ± SD) was 50.2% ± 2.4% in healthy subjects and 53.5% ± 5.6% in infected patients. Mean ± SD tebipenem pharmacokinetic parameters in plasma for healthy subjects and infected patients were: maximum free concentration (fCmax), 3.74 ± 2.35 and 3.40 ± 2.86 mg/L, respectively; half-life, 0.88 ± 0.11 and 2.02 ± 1.32 h; fAUC0–8, 5.61 ± 1.64 and 10.01 ± 4.81 mg·h/L. Tebipenem tissue AUC0–8 was 5.99 ± 3.07 and 8.60 ± 2.88 mg·h/L for healthy subjects and patients, respectively. The interstitial concentration–time profile largely mirrored the free plasma profile within both populations, resulting in a penetration ratio of 107% in healthy subjects and 90% in infected patients.

Conclusions
Tebipenem demonstrated excellent distribution into skin and soft tissue of healthy subjects and patients with DFI following oral administration of 600 mg of tebipenem pivoxil hydrobromide.
BGLM: big data-guided LOINC mapping with multi-language support
Authors: Liu Ke , Witteveen-Lane Martin , Glicksberg Benjamin S , Kulkarni Omkar , Shankar Rama , Chekalin Evgeny , Paithankar Shreya , Yang Jeanne , Chesla Dave , Chen Bin 
Published: November 2022

Abstract

Motivation
Mapping internal, locally used lab test codes to standardized logical observation identifiers names and codes (LOINC) terminology has become an essential step in harmonizing electronic health record (EHR) data across different institutions. However, most existing LOINC code mappers are based on text-mining technology and do not provide robust multi-language support.

Materials and methods
We introduce a simple, yet effective tool called big data-guided LOINC code mapper (BGLM), which leverages the large amount of patient data stored in EHR systems to perform LOINC coding mapping. Distinguishing from existing methods, BGLM conducts mapping based on distributional similarity.

Results
We validated the performance of BGLM with real-world datasets and showed that high mapping precision could be achieved under proper false discovery rate control. In addition, we showed that the mapping results of BGLM could be used to boost the performance of Regenstrief LOINC Mapping Assistant (RELMA), one of the most widely used LOINC code mappers.

Conclusions
BGLM paves a new way for LOINC code mapping and therefore could be applied to EHR systems without the restriction of languages. BGLM is freely available at https://github.com/Bin-Chen-Lab/BGLM.
Spatial separation of phosphatase and kinase activity within the Bub complex is required for proper mitosis
Authors: Wang Lei , Kruse Thomas , López-Méndez Blanca , Zhang Yuqing , Song Chunlin , Zhu Lei , Li Bing , Fang Jing , Lu Zhimin , Nilsson Jakob , Zhang Gang 
Published: November 2022

ABSTRACT
The Bub1 and BubR1 kinetochore proteins support proper chromosome segregation and mitotic checkpoint activity. Bub1 and BubR1 are paralogs with Bub1 being a kinase, while BubR1 localizes the PP2A-B56 protein phosphatase to kinetochores in humans. Whether this spatial separation of kinase and phosphatase activity is important is unclear as some organisms integrate both activities into one Bub protein. Here, we engineer human Bub1 and BubR1 proteins integrating kinase and phosphatase activities into one protein and show that these do not support normal mitotic progression. A Bub1–PP2A-B56 complex can support chromosome alignment but results in impairment of the checkpoint due to dephosphorylation of the Mad1 binding site in Bub1. Furthermore, a chimeric BubR1 protein containing the Bub1 kinase domain induces delocalized H2ApT120 phosphorylation, resulting in the reduction of centromeric hSgo2 and chromosome segregation errors. Collectively, these results argue that the spatial separation of kinase and phosphatase activities within the Bub complex is required for balancing its functions in the checkpoint and chromosome alignment.
On the response of eccentric non-structures subjected to horizontal oscillation
Authors: Su Liang-Shen , Lin Chi-Hao , Chen Kuo-Ching 
Published: November 2022

ABSTRACTIn contrast to building structures, little attention has been paid to the seismic performance of non-structures in buildings, especially of eccentric non-structures. This paper attempts to explore the rocking and overturning of eccentric blocks, which could be the equipment or non-structural components in buildings, subjected to horizontal vibration. In the present study, a non-structure is regarded as a rigid block with tunable mass eccentricity, and the contact friction is assumed to be large enough to prevent the rigid block from sliding. A free shaking test is first carried out to determine the value of the coefficient of restitution. Force oscillations are then investigated to determine the critical time and acceleration when the eccentric blocks fall down under the swept-frequency oscillation. Finally, an actual acceleration from the seismic records is executed on each of the eccentric blocks to measure and to explore the corresponding toppling probability. It is found that the toppling of blocks is not necessarily linked to the magnitude of the peak ground acceleration.
Article 6
Authors: Chuang Janie , Sarugaser-Hug Sulini 
Published: November 2022

Abstract
This chapter describes Article 6 of the Convention on the Elimination of All Forms of Discrimination against Women (CEDAW), which addresses the obligation of States parties to suppress the trafficking and exploitation of the prostitution of women. The CEDAW Committee frames trafficking as a form of gender-based violence that persists due to States parties’ failure to effectively address its root causes, which lie in sex-based discrimination and the prevailing economic and patriarchal structures as well as the adverse and gender-differentiated impact of labour, migration, and asylum regimes. However, General Recommendation No 38 reflects a tension between such a transformative vision and a narrower approach that views women as victims and the State as protector. General Recommendation No 38 does a particular disservice to sex workers, undermining their rights, denying their agency, and negating the powerful role they can play in the fight against trafficking. Ultimately, the extent to which the Committee has brought cohesiveness and clarity to States parties’ understanding of their obligations under international law to supress the exploitation of prostitution of women is dubious.
Article 7
Authors: Wittkopp Sarah 
Published: November 2022

Abstract
This chapter explores Article 7 of the Convention on the Elimination of All Forms of Discrimination against Women (CEDAW), which comprehensively addresses States parties’ obligations in realizing women’s political rights. These include the right to participate directly in the formulation of public policy as elected representatives (Article 7(a)) or as appointed public officials (Article 7(b)), as well as indirectly through voting (Article 7(a)). Article 7 is unique in human rights law because it also encompasses non-discrimination with regard to the participation in non-governmental organizations and associations (Article 7(c)). In these respects, States parties must strive to realize formal, substantive, and transformative equality which includes the adoption of temporary special measures (TSMs) under Article 4(1) to accelerate its realization. The chapter analyses how the CEDAW Committee has interpreted the meaning and scope of States parties’ obligations under the article in its concluding observations and general recommendations. It states that the obligation to reach substantive equality in political and public life requires States parties to reach parity between men and women by 2030, even if its jurisprudence remains wavering.
Article 10
Authors: Bailey Barbara , Gbedemah Hilary 
Published: November 2022

Abstract
This chapter highlights Article 10 of the Convention on the Elimination of All Forms of Discrimination against Women (CEDAW). Article 10, the right to education, is the first of the five articles included in the third part of the CEDAW Convention devoted to the economic, social, and cultural rights of women. CEDAW’s General Recommendation No 36 (adopted in 2017) on the rights of girls and women to education and numerous concluding observations urge States parties to enhance compliance with Article 10 and ‘raise awareness of the importance of education as a human right and as the basis for the empowerment of women’. In addition to a life-cycle approach to education by which states are to ensure equal rights between men and women in education from pre-school through general, technical, vocational, higher, and professional education, Article 10 imposes positive and negative obligations on states to respect, protect, and fulfil the obligations laid out in this article. There is no reservation to Article 10. However, careful scrutiny of national legislation and policies must ensure that they do not contain claw-back provisions to the article and that legislation and policies on education are gender-sensitive and integrate gender equality into education at all levels.
Article 15
Authors: Narain Aruna D 
Published: November 2022

Abstract
This chapter details Article 15 of the Convention on the Elimination of All Forms of Discrimination against Women (CEDAW). Article 15(1) states in simple and explicit language the norm on equality between men and women before the law that underpins the entire Convention. Article 15(1) is followed by additional provisions which deal with equality in regard to women’s legal capacity in specific areas of civil law and the same right as men to acquire a domicile and, by implication, to be governed by a legal system of their choice through freedom of movement and residence. This article must be understood in the context of the evolving meaning of the concept of ‘equality before the law’. Constitutional provisions on equality in domestic jurisdictions and international human rights instruments use the phrase ‘equality before the law’ and ‘equal protection of the law’. The CEDAW Committee has elaborated that Article 15 provides that women and men must have equality before the law as well as benefit from equal protection of the law.