bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of transcriptomics biomarkers for the early prediction of the prognosis of septic shock from pneumopathies
Authors: Shi Songchang , Pan Xiaobin , Feng Hangwei , Zhang Shujuan , Shi Songjing , Lin Wei 
Published: November 2021

Abstract
Background
Identifying the biological subclasses of septic shock might provide specific targeted therapies for the treatment and prognosis of septic shock. It might be possible to find biological markers for the early prediction of septic shock prognosis.

Methods
The data were obtained from the Gene Expression Omnibus databases (GEO) in NCBI. GO enrichment and KEGG pathway analyses were performed to investigate the functional annotation of up- and downregulated DEGs. ROC curves were drawn, and their areas under the curves (AUCs) were determined to evaluate the predictive value of the key genes.

Results
117 DEGs were obtained, including 36 up- and 81 downregulated DEGs. The AUC for the MME gene was 0.879, as a key gene with the most obvious upregulation in septic shock. The AUC for the THBS1 gene was 0.889, as a key downregulated gene with the most obvious downregulation in septic shock.

Conclusions
The upregulation of MME via the renin-angiotensin system pathway and the downregulation of THBS1 through the PI3K–Akt signaling pathway might have implications for the early prediction of prognosis of septic shock in patients with pneumopathies.
Impact of socio-economic factors on Tuberculosis treatment outcomes in north-eastern Uganda: a mixed methods study
Authors: Nidoi Jasper , Muttamba Winters , Walusimbi Simon , Imoko Joseph F. , Lochoro Peter , Ictho Jerry , Mugenyi Levicatus , Sekibira Rogers , Turyahabwe Stavia , Byaruhanga Raymond , Putoto Giovanni , Villa Simone , Raviglione Mario C. , Kirenga Bruce 
Published: November 2021

Abstract
Background
Tuberculosis (TB) is a major public health problem and at 48%, Karamoja in North-Eastern Uganda has the lowest treatment success rate nationally. Addressing the social determinants of TB is crucial to ending TB. This study sought to understand the extent and ways in which socio-economic factors affect TB treatment outcomes in Karamoja.

Methods
We conducted a convergent parallel mixed methods study in 10 TB Diagnostic and Treatment Units. The study enrolled former TB patients diagnosed with drug-susceptible TB between April 2018 and March 2019. Unit TB and laboratory registers were reviewed to identify pre-treatment losses to follow-up. Four focus group discussions with former TB patients and 18 key informant interviews with healthcare workers were conducted. Principle component analysis was used to generate wealth quintiles that were compared to treatment outcomes using the proportion test. The association between sociodemographic characteristics and TB treatment outcomes was evaluated using the chi-square test and multiple logistic regression.

Results
A total of 313 participants were randomly selected from 1184 former TB patients recorded in the unit TB registers. Of these, 264 were contacted in the community and consented to join the study: 57% were male and 156 (59.1%) participants had unsuccessful treatment outcomes. The wealthiest quintile had a 58% reduction in the risk of having an unsuccessful treatment outcome (adj OR = 0.42, 95% CI 0.18–0.99, p = 0.047). People who were employed in the informal sector (adj OR = 4.71, 95% CI 1.18–18.89, p = 0.029) and children under the age of 15 years who were not in school or employed (adj OR = 2.71, 95% CI 1.11–6.62, p = 0.029) had significantly higher odds of unsuccessful treatment outcome. Analysis of the pre-treatment loss to follow-up showed that 17.2% of patients with pulmonary bacteriologically confirmed TB did not initiate treatment with a higher proportion among females (21.7%) than males (13.5%). Inadequate food, belonging to migratory communities, stigma, lack of social protection, drug stock-outs and transport challenges affected TB treatment outcomes.

Conclusions
This study confirmed that low socio-economic status is associated with poor TB treatment outcomes emphasizing the need for multi- and cross-sectoral approaches and socio-economic enablers to optimise TB care.
Pedicle screw accuracy in thoracolumbar fractures- is routine postoperative CT scan necessary?
Authors: Aigner R. , Bichlmaier C. , Oberkircher L. , Knauf T. , König A. , Lechler P. , Ruchholtz S. , Frink M. 
Published: November 2021

Abstract
Background
While several studies report on accuracy rates of pedicle screws, risk factors associated with inaccurate pedicle screw positioning in patients with thoracolumbar fractures are reported rarely. CT scan as a routine postoperative control is advocated by various authors, however its necessity remains unclear.

Methods
Two hundred forty-five patients were included in this retrospective study. Percutaneous dorsal instrumentation was most commonly performed (n = 201). Classification of Zdichavsky et al. and Rao et al. were used to classify screw misplacement and anterior perforation was further evaluated according to the extent of perforation (< 2 mm; > 2 mm). Multivariate analysis was performed to identify risk factors for misplacement of screws.

Results
One thousand sixty-eight pedicle screws were inserted in 245 patients. Misplacement was found in 51 screws (4.8%) in 42 patients (17.1%) according to the classification of Zdichavsky et al. and in 75 screws (7.0%) in 64 patients (26.1%) according to the classification of Rao et al.. An anterior perforation of the vertebral cortex was found in 56 screws (5.2%). Multivariate analysis showed fracture location in the upper thoracic (p = 0.048) and lumbar spine (p = 0.013) to be the only independent predictors for screw misplacement. In addition a significant correlation between pedicle diameter and the occurrence of screw malposition was found (p = 0.003). No consequences were drawn from postoperative routine CT in asymptomatic patients.

Conclusion
An overall low rate of screw misplacement was found with fracture location in the upper thoracic and lumbar spine being the only factors independently associated with the risk of screw misplacement. No consequences were drawn from postoperative routine CT in asymptomatic patients. Therefore its use has to be discussed critically.
Potentilla reptans L. postconditioning protects reperfusion injury via the RISK/SAFE pathways in an isolated rat heart
Authors: Enayati Ayesheh , Salehi Aref , Alilou Mostafa , Stuppner Hermann , Polshekan Mirali , Rajaei Maryam , Pourabouk Mona , Jabbari Ali , Mazaheri Zohreh , Yassa Narguess , Moheimani Hamid Reza , Khori Vahid 
Published: November 2021

Abstract
Background
Our previous study indicated that Potentilla reptans root has a preconditioning effect by its antioxidant and anti-apoptotic effects in an isolated rat heart ischemia/reperfusion (IR) model. In the present study, we investigated the post-conditioning cardio-protective effects of Potentilla reptans and its active substances.

Methods
The ethyl acetate fraction of P. reptans root (Et) was subjected to an IR model under 30 min of ischemia and 100 min of reperfusion. To investigate the postconditioning effect, Et was perfused for 15 min at the early phase of reperfusion. RISK/SAFE pathway inhibitors, 5HD and L-NAME, were applied individually 10 min before the ischemia, either alone or in combination with Et during the early reperfusion phase. The hemodynamic factors and ventricular arrhythmia were calculated during the reperfusion. Oxidative stress, apoptosis markers, GSK-3β and SGK1 proteins were assessed at the end of experiments.

Results
Et postconditioning (Etpost) significantly reduced the infarct size, arrhythmia score, ventricular fibrillation incidence, and enhanced the hemodynamic parameters by decreasing the MDA level and increasing expression of Nrf2, SOD and CAT activities. Meanwhile, Etpost increased the BCl-2/BAX ratio and decreased Caspase-3 expression. The cardioprotective effect of Etpost was abrogated by L-NAME, Wortmannin (a PI3K/Akt inhibitor), and AG490 (a JAK/STAT3 inhibitor). Finally, Etpost reduced the expression of GSK-3β and SGK1 proteins pertaining to the IR group.

Conclusion
P. reptans reveals the post-conditioning effects via the Nrf2 pathway, NO release, and the RISK/SAFE pathway. Also, Etpost decreased apoptotic indexes by inhibiting GSK-3β and SGK1 expressions. Hence, our data suggest that Etpost can be a suitable natural candidate to protect cardiomyocytes during reperfusion injury.
The impact of “4 + 7” volume-based drug procurement on the volume, expenditures, and daily costs of antihypertensive drugs in Shenzhen, China: an interrupted time series analysis
Authors: Yang Ying , Tong Ruiwen , Yin Shicheng , Mao Lining , Xu Luxinyi , Hao Siyu , Mao Zongfu 
Published: November 2021

Abstract
Background
In 2019, Chinese government launched a nationwide volume-based drug procurement aiming at reducing drug prices and saving drug costs through economies of scale, which aroused widespread attention. The first round of the policy pilot was implemented in 4 municipalities and 7 sub-provincial cities, referred to as “4 + 7” policy. In the “4 + 7” policy, 7 antihypertensive drugs were included. This study was conducted to evaluate the impact of “4 + 7” policy on the use of policy-related antihypertensive drugs.

Method
This study applied single-group Interrupted Time Series (ITS) design. We used drug purchasing data from the Centralized Drug Procurement Survey in Shenzhen 2019, covering 24 months from January 2018 to December 2019. Antihypertensive drugs related to “4 + 7” policy were selected as study samples, including 7 drugs in the “4 + 7” List and 17 alternative drugs. Alternative drugs refer to antihypertensive drugs that have an alternative relationship with “4 + 7” List drugs in clinical use and have not yet been covered by the policy. “4 + 7” List drugs were then divided into bid-winning and bid-non-winning products according to the bidding results. Purchase volume, expenditures, and daily costs were selected as outcome variables, and were measured using Defined Daily Doses (DDDs), Chinese Yuan (CNY), and Defined Daily Drug cost (DDDc).

Results
After “4 + 7” policy intervention, the procurement volume of bid-winning antihypertensive drugs significantly increased (3.12 million DDD, 95 % CI = 2.14 to 4.10, p < 0.001), while the volume of non-winning drugs decreased (-2.33 million DDD, 95 % CI= -2.83 to -1.82, p < 0.01). The use proportion of bid-winning antihypertensive drugs increased from 12.31 to 87.74 % after policy intervention. The overall costs of the seven “4 + 7” List antihypertensive drugs significantly declined (-5.96 million CNY, 95 % CI= -7.87 to -4.04, p < 0.001) after policy intervention, with an absolute reduction of 36.37 million CNY compared with the pre-“4 + 7” period. The DDDc of bid-winning antihypertensive drugs significantly decreased (-1.30 CNY, 95 % CI= -1.43 to -1.18, p < 0.001), while the DDDc of non-winning (0.28 CNY, 95 % CI = 0.11 to 0.46, p < 0.01) and alternative (0.14 CNY, 95 % CI = 0.03 to 0.25, p < 0.05) antihypertensive drugs increased markedly.

Conclusions
The implementation of “4 + 7” policy promoted the drug use hypertensive patients gradually concentrated on the quality-guaranteed bid-winning drugs, which might be conducive to improve the overall quality level of drug use of Chinese hypertensive patients. Besides, a preliminary positive policy effect of price cut and cost-saving was observed in the antihypertensive drug category. In the future, price monitoring and drug use management regarding policy-related drugs should also be strengthened.
Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae
Authors: Petersen Malte , Winter Sven , Coimbra Raphael , J. de Jong Menno , Kapitonov Vladimir V. , Nilsson Maria A. 
Published: November 2021

Abstract
Background
The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species.

Results
The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories.

Conclusions
The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.
Discussing human values in digital immortality: towards a value-oriented perspective
Authors: Galvão Vinícius Ferreira , Maciel Cristiano , Pereira Roberto , Gasparini Isabela , Viterbo José , Bicharra Garcia Ana Cristina 
Published: November 2021

AbstractIntense social media interaction, wearable devices, mobile applications, and pervasive use of sensors have created a personal information ecosystem for gathering traces of individual behavior. These traces are the digital legacy individuals build all through their lives. Advances in artificial intelligence have fed our dream to build artificial agents trained with these digital traces to behave similarly to a deceased person, and individuals are facing the possibility of immortalizing their ideas, reasoning and behavior. Are people prepared for that? Are people willing to do that? How do people perceive the possibility of letting digital avatars take care of their digital legacy? This paper sheds light on these questions by discussing users’ perceptions towards digital immortality in a focus group analysis with 8 participants. Our findings suggest some key human values must be addressed. These findings can serve as preliminary thoughts to inform system design, from the very early stage of development, that preserve the digital legacy while respecting the human needs and values concerning the delicate emotional moment that death provides. This qualitative research analyzes the data, and based on the insights learned, proposes important considerations for future developments in this area.
Remarkably coherent population structure for a dominant Antarctic Chlorobium species
Authors: Panwar Pratibha , Allen Michelle A. , Williams Timothy J. , Haque Sabrina , Brazendale Sarah , Hancock Alyce M. , Paez-Espino David , Cavicchioli Ricardo 
Published: November 2021

AbstractBackgroundIn Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby “feeding” ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, aChlorobiumspecies of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59Chlorobiummetagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function.ResultsA single species,CandidatusChlorobium antarcticum (most similar toChlorobium phaeovibrioidesDSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108cells ml−1in Ace Lake) and seasonal cycle of cell lysis likely makeCa.Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis ofCa.Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease inCa.Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts.ConclusionThe factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. TheChlorobiumpopulation studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in thisChlorobiumspecies.
Behaviour, temperature and terrain slope impact estimates of energy expenditure using oxygen and dynamic body acceleration
Authors: Dickinson Eleanor R. , Stephens Philip A. , Marks Nikki J. , Wilson Rory P. , Scantlebury David M. 
Published: November 2021

AbstractThe energy used by animals is influenced by intrinsic (e.g. physiological) and extrinsic (e.g. environmental) factors. Accelerometers within biologging devices have proven useful for assessing energy expenditures and their behavioural context in free-ranging animals. However, certain assumptions are frequently made when acceleration is used as a proxy for energy expenditure, with factors, such as environmental variation (e.g. ambient temperature or slope of terrain), seldom accounted for. To determine the possible interactions between behaviour, energy expenditure and the environment (ambient temperature and terrain slope), the rate of oxygen consumption ($${\dot{\text{V}}\text{O}}_{2}$$V˙O2) was measured in pygmy goats (Capra hircus aegarus) using open-flow indirect calorimetry. The effect of temperature (9.7–31.5 °C) on resting energy expenditure was measured. The relationship between$${\dot{\text{V}}\text{O}}_{2}$$V˙O2and dynamic body acceleration (DBA) was measured at different walking speeds (0.8–3.0 km h−1) and on different inclines (0, + 15°, − 15°). The daily behaviour of individuals was measured in two enclosures: enclosure A (level terrain during summer) and enclosure B (sloped terrain during winter) andper diemenergy expenditures of behaviours estimated using behaviour, DBA, temperature, terrain slope and$${\dot{\text{V}}\text{O}}_{2}$$V˙O2. During rest, energy expenditure increased below 22 °C and above 30.5 °C.$${\dot{\text{V}}\text{O}}_{2}$$V˙O2(ml min−1) increased with DBA when walking on the level. Walking uphill (+ 15°) increased energetic costs three-fold, whereas walking downhill (− 15°) increased energetic costs by one third. Based on these results, although activity levels were higher in animals in enclosure A during summer, energy expenditure was found to be significantly higher in the sloped enclosure B in winter (means of enclosures A and B: 485.3 ± 103.6 kJ day−1and 744.5 ± 132.4 kJ day−1). We show that it is essential to account for extrinsic factors when calculating animal energy budgets. Our estimates of the impacts of extrinsic factors should be applicable to other free ranging ungulates.
CMOS voltage-controlled oscillator with high-performance MEMS tunable inductor
Authors: Chae Uikyu , Park Jeongsoo , Kim Jeong-Geun , Yu Hyun-Yong , Cho Il-Joo 
Published: November 2021

AbstractLC CMOS voltage-controlled oscillators (VCOs) with tunable inductors are essential for high-performance, multi-band communication systems, such as IoT applications and 5G communication. However, VCOs that use CMOS tunable inductors have difficulty in achieving high RF performance due to the low Q-factor of the inductor. In addition, previously reported CMOS VCOs integrated with MEMS inductors have used CMOS switches for tuning frequency bands, but they also had large signal losses on the switch. Herein, we propose a CMOS VCO that is integrated with a MEMS tunable inductor that tunes the frequency band with three MEMS switches. The proposed MEMS tunable inductor enables us to achieve high RF performance due to the suspended structure, and RF MEMS switches enable lower signal loss than CMOS switches. In this work, we successfully fabricated the proposed CMOS VCO integrated with a MEMS tunable inductor using the flip-chip bonding process, and we measured oscillation frequencies according to the actuation of the three switches. The oscillation powers were measured as − 3.03 dBm @ 1.39 GHz, − 5.80 @ 1.98 GHz, − 7.44 dBm @ 2.81 GHz, and − 8.77 dBm @ 3.68 GHz.
Role of the eastern boundary-generated waves on the termination of 1997 Indian Ocean Dipole event
Authors: Iskandar Iskhaq , Nagura Motoki , McPhaden Michael J. 
Published: November 2021

AbstractThe termination of Indian Ocean Dipole (IOD) events is examined in terms of equatorial wave dynamics. In situ and satellite observations combined with an output from a linear wave model are used in this study. Our emphasis is on the 1997 IOD event but our results apply to other positive IOD events as well. We find that the termination of anomalously cold sea surface temperature (SST) in the eastern pole of the dipole is associated with a warming tendency caused by the net surface heat fluxes. However, net surface heat fluxes alone cannot explain the total change in the SST. We show that during the peak phase of an IOD event, the weakening of zonal heat advection caused by eastern boundary-generated Rossby waves combined with the reduction of vertical entrainment and diffusion creates favorable conditions for surface heat fluxes to warm the SST in the eastern basin.