bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing public–private procurement practices for medical commodities in Dar Es Salaam: a situation analysis
Authors: Mbwasi Romuald , Mbepera Denis , Mfuko William , Makanzo Jason , Kikwale Martha , Canavan Robert , Stoermer Manfred , Wiedenmayer Karin 
Published: December 2022

Abstract
Background
In Tanzania, the Medical Stores Department is the principal pharmaceutical provider to public health facilities throughout the country. However, growing demand from health facilities has proved difficult to satisfy and stock-outs at health facilities are frequent. The aim of the current study was to conduct a situation analysis of the procedures and practices of procuring medicines and medical supplies from private suppliers in the Dar es Salaam region when those commodities are unavailable at the Medical Stores Department.

Methods
A mixed-method approach including qualitative and quantitative methods was applied to understand procurement procedures and practices and private suppliers’ performance at district level. Qualitative interviews with suppliers and district authorities, and a review of inventory documents at store level was conducted between February and March 2018. The quantitative approach included a review and analyses of relevant procurement documents from the 2016/2017 financial year to explore the funds used to procure health commodities from the private sector. The ten most frequently mandated private suppliers were assessed in more detail focusing on cost, quality and availability of medicines and lead times and delivery.

Results
A lack of consistency and written guidelines for procuring medicines and medical supplies from the private sector was observed. The procurement process was bureaucratic and lengthy requiring multiple steps between health facilities, suppliers and district authorities. A significant number of people were involved requiring a minimum of 13 signatures and 16 steps from order preparation to approval.
Only 17 of 77 prequalified private suppliers received orders from public health facilities. The criteria for choosing which supplier to use were unclear. Completed orders amounted to USD 663,491. The bureaucratic process drove councils and healthcare facilities towards alternative ways to procure health commodities when Medical Stores Department stock-outs occurred.

Conclusion
The procurement procedure outside the Medical Stores Department is inefficient and cumbersome, often circumventing government regulations. General lack of accountability renders the process susceptible to leakage of funds and medicines. Increasing the transparency and efficiency of procurement procedures from the private sector with a prime vendor system would help to better manage Medical Stores Department stock-outs and help improve health care services overall.
Stigma experienced by people living with HIV who are on methadone maintenance treatment and have symptoms of common mental disorders in Hanoi, Vietnam: a qualitative study
Authors: Tran Ha V. , Filipowicz Teresa R. , Landrum Kelsey R. , Nong Ha T. T. , Tran Thuy T. T. , Pence Brian W. , Go Vivian F. , Le Giang M. , Nguyen Minh X. , Verhey Ruth , Chibanda Dixon , Ho Hien T. , Gaynes Bradley N. 
Published: December 2022

Abstract
Background
Stigma around human immunodeficiency virus (HIV), injection drug use (IDU), and mental health disorders can be co-occurring and have different impacts on the well-being of people living with HIV (PWH) who use drugs and have mental health disorders. This stigma can come from society, health professionals, and internalized stigma. A person who has more than one health condition can experience overlapping health-related stigma and levels of stigma which can prevent them from receiving necessary support and healthcare, serving to intensify their experience with stigma. This study investigates HIV, drug use, and mental health stigmas in three dimensions (social, internalized, and professional) around PWH on methadone maintenance treatment (MMT) who have common mental disorders (CMDs) including depression, anxiety, and stress-related disorders in Hanoi, Vietnam.Please check and confirm whether corresponding author's email id is correctly identified.The cooresponding author's email is correct

Methods
We conducted semi-structured, in-depth interviews (IDIs) (n = 21) and two focus group discussions (FGDs) (n = 10) with PWH receiving MMT who have CMD symptoms, their family members, clinic health care providers, and clinic directors. We applied thematic analysis using NVIVO software version 12.0, with themes based on IDI and FGD guides and emergent themes from interview transcripts.

Results
The study found evidence of different stigmas towards HIV, IDU, and CMDs from the community, family, health care providers, and participants themselves. Community and family members were physically and emotionally distant from patients due to societal stigma around illicit drug use and fears of acquiring HIV. Participants often conflated stigmas around drug use and HIV, referring to these stigmas interchangeably. The internalized stigma around having HIV and injecting drugs made PWH on MMT hesitant to seek support for CMDs. These stigmas compounded to negatively impact participants’ health.

Conclusions
Strategies to reduce stigma affecting PWH on MMT should concurrently address stigmas around HIV, drug addiction, and mental health. Future studies could explore approaches to address internalized stigma to improve self-esteem, mental health, and capacities to cope with stigma for PWH on MMT.
Trial registration: NCT04790201, available at clinicaltrials.gov.
Is VATS approach suitable in re-operations for postoperative hemothorax after pulmonary resection? Data analysis in a big volume thoracic center
Authors: Li Zhixin , Wu Lei-Lei , Gao Jiani , Wang Yichao , Zhao Xiaogang , Xie Dong 
Published: December 2022

Abstract
Objective
This study explored the safety and of feasibility of video-assisted thoracoscopy (VATS) in re-operations for post-operative hemothorax.

Methods
The clinical data of patients underwent re-operations due to post-operative hemothorax after pulmonary resection in Shanghai Pulmonary Hospital from 2006 to 2018 were retrospectively analysed. The incidence of re-operations were analyzed. The mortality and morbidity were compared between thoracotomy and thoracoscopic procedure for re-exploration.

Results
A total of 114 patients were included. The annual incidence rate ranged from 0.21 to 0.54%; the perioperative mortality was 2.6%; there were 114 cases of re-operations for hemothorax after 2012, including 62 cases in thoracoscopy group and 52 cases in open group. The durations of chest-tube drainage (7.2 ± 3.9 days vs 10.9 ± 12.0 days, P = 0.001) and length of stay in hospital (13.7 ± 6.7 days vs 18.9 ± 10.6 days, P = 0.002) in the thoracoscopic group were shorter than those in the open group. The thoracoscopic group had fewer post-operative complications as well (P = 0.023). Meanwhile, post-operative complications in the delayed group were significantly higher than those in the non-delayed group, with a longer length of hospital stay and higher hospitalization costs.

Conclusion
Complete VATS is safe and feasible for re-operation due to post-operative hemothorax and can be an alternative to thoracotomy. Delayed re-operations are associated with more post-operative complications and higher costs.
Metabolic engineering of Corynebacterium glutamicum for acetate-based itaconic acid production
Authors: Schmollack Marc , Werner Felix , Huber Janine , Kiefer Dirk , Merkel Manuel , Hausmann Rudolf , Siebert Daniel , Blombach Bastian 
Published: December 2022

Abstract
Background
Itaconic acid is a promising platform chemical for a bio-based polymer industry. Today, itaconic acid is biotechnologically produced with Aspergillus terreus at industrial scale from sugars. The production of fuels but also of chemicals from food substrates is a dilemma since future processes should rely on carbon sources which do not compete for food or feed. Therefore, the production of chemicals from alternative substrates such as acetate is desirable to develop novel value chains in the bioeconomy.

Results
In this study, Corynebacterium glutamicum ATCC 13032 was engineered to efficiently produce itaconic acid from the non-food substrate acetate. Therefore, we rewired the central carbon and nitrogen metabolism by inactivating the transcriptional regulator RamB, reducing the activity of isocitrate dehydrogenase, deletion of the gdh gene encoding glutamate dehydrogenase and overexpression of cis-aconitate decarboxylase (CAD) from A. terreus optimized for expression in C. glutamicum. The final strain C. glutamicum ΔramB Δgdh IDHR453C (pEKEx2-malEcadopt) produced 3.43 ± 0.59 g itaconic acid L−1 with a product yield of 81 ± 9 mmol mol−1 during small-scale cultivations in nitrogen-limited minimal medium containing acetate as sole carbon and energy source. Lowering the cultivation temperature from 30 °C to 25 °C improved CAD activity and further increased the titer and product yield to 5.01 ± 0.67 g L−1 and 116 ± 15 mmol mol−1, respectively. The latter corresponds to 35% of the theoretical maximum and so far represents the highest product yield for acetate-based itaconic acid production. Further, the optimized strain C. glutamicum ΔramB Δgdh IDHR453C (pEKEx2-malEcadopt), produced 3.38 ± 0.28 g itaconic acid L−1 at 25 °C from an acetate-containing aqueous side-stream of fast pyrolysis.

Conclusion
As shown in this study, acetate represents a suitable non-food carbon source for itaconic acid production with C. glutamicum. Tailoring the central carbon and nitrogen metabolism enabled the efficient production of itaconic acid from acetate and therefore this study offers useful design principles to genetically engineer C. glutamicum for other products from acetate.
Loss of Y in leukocytes as a risk factor for critical COVID-19 in men
Authors: Bruhn-Olszewska Bożena , Davies Hanna , Sarkisyan Daniil , Juhas Ulana , Rychlicka-Buniowska Edyta , Wójcik Magdalena , Horbacz Monika , Jąkalski Marcin , Olszewski Paweł , Westholm Jakub O. , Smialowska Agata , Wierzba Karol , Torinsson Naluai Åsa , Jern Niklas , Andersson Lars-Magnus , Järhult Josef D. , Filipowicz Natalia , Tiensuu Janson Eva , Rubertsson Sten , Lipcsey Miklós , Gisslén Magnus , Hultström Michael , Frithiof Robert , Dumanski Jan P. 
Published: December 2022

AbstractBackgroundThe COVID-19 pandemic, which has a prominent social and economic impact worldwide, shows a largely unexplained male bias for the severity and mortality of the disease. Loss of chromosome Y (LOY) is a risk factor candidate in COVID-19 due to its prior association with many chronic age-related diseases, and its impact on immune gene transcription.MethodsPublicly available scRNA-seq data of PBMC samples derived from male patients critically ill with COVID-19 were reanalyzed, and LOY status was added to the annotated cells. We further studied LOY in whole blood for 211 COVID-19 patients treated at intensive care units (ICU) from the first and second waves of the pandemic. Of these, 139 patients were subject to cell sorting for LOY analysis in granulocytes, low-density neutrophils (LDNs), monocytes, and PBMCs.ResultsReanalysis of available scRNA-seq data revealed LDNs and monocytes as the cell types most affected by LOY. Subsequently, DNA analysis indicated that 46%, 32%, and 29% of critically ill patients showed LOY above 5% cut-off in LDNs, granulocytes, and monocytes, respectively. Hence, the myeloid lineage that is crucial for the development of severe COVID-19 phenotype is affected by LOY. Moreover, LOY correlated with increasing WHO score (median difference 1.59%, 95% HDI 0.46% to 2.71%,p=0.025), death during ICU treatment (median difference 1.46%, 95% HDI 0.47% to 2.43%,p=0.0036), and history of vessel disease (median difference 2.16%, 95% HDI 0.74% to 3.7%,p=0.004), among other variables. In 16 recovered patients, sampled during ICU stay and 93–143 days later, LOY decreased significantly in whole blood and PBMCs. Furthermore, the number of LDNs at the recovery stage decreased dramatically (median difference 76.4 per 10,000 cell sorting events, 95% HDI 55.5 to 104,p=6e−11).ConclusionsWe present a link between LOY and an acute, life-threatening infectious disease. Furthermore, this study highlights LOY as the most prominent clonal mutation affecting the myeloid cell lineage during emergency myelopoiesis. The correlation between LOY level and COVID-19 severity might suggest that this mutation affects the functions of monocytes and neutrophils, which could have consequences for male innate immunity.
Granulovacuolar degeneration bodies are independently induced by tau and α-synuclein pathology
Authors: Jorge-Oliva Marta , Smits Jasper F. M. , Wiersma Vera I. , Hoozemans Jeroen J. M. , Scheper Wiep 
Published: December 2022

Abstract
Background
Granulovacuolar degeneration bodies (GVBs) are intracellular vesicular structures that commonly accompany pathological tau accumulations in neurons of patients with tauopathies. Recently, we developed the first model for GVBs in primary neurons, that requires exogenous tau seeds to elicit tau aggregation. This model allowed the identification of GVBs as proteolytically active lysosomes induced by tau pathology. GVBs selectively accumulate cargo in a dense core, that shows differential and inconsistent immunopositivity for (phosphorylated) tau epitopes. Despite the strong evidence connecting GVBs to tau pathology, these structures have been reported in neurons without apparent pathology in brain tissue of tauopathy patients. Additionally, GVBs and putative GVBs have also been reported in the brain of patients with non-tau proteinopathies. Here, we investigated the connection between pathological protein assemblies and GVBs in more detail.

Methods
This study combined newly developed primary neuron models for tau and α-synuclein pathology with observations in human brain tissue from tauopathy and Parkinson’s disease patients. Immunolabeling and imaging techniques were employed for extensive characterisation of pathological proteins and GVBs. Quantitative data were obtained by high-content automated microscopy as well as single-cell analysis of confocal images.

Results
Employing a novel seed-independent neuronal tau/GVB model, we show that in the context of tauopathy, GVBs are inseparably associated with the presence of cytosolic pathological tau and that intracellular tau aggregation precedes GVB formation, strengthening the causal relationship between pathological accumulation of tau and GVBs. We also report that GVBs are inseparably associated with pathological tau at the single-cell level in the hippocampus of tauopathy patients. Paradoxically, we demonstrate the presence of GVBs in the substantia nigra of Parkinson’s disease patients and in a primary neuron model for α-synuclein pathology. GVBs in this newly developed α-synuclein/GVB model are induced in the absence of cytosolic pathological tau accumulations. GVBs in the context of tau or α-synuclein pathology showed similar immunoreactivity for different phosphorylated tau epitopes. The phosphorylated tau immunoreactivity signature of GVBs is therefore independent of the presence of cytosolic tau pathology.

Conclusion
Our data identify the emergence of GVBs as a more generalised response to cytosolic protein pathology.
Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: a review
Authors: Mak Philip H. W. , Rehman Muhammad Attiq , Kiarie Elijah G. , Topp Edward , Diarra Moussa S. 
Published: December 2022

AbstractEconomic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers, despite substantial efforts in prevention and control. Antibiotics have been used not only for the treatment and prevention of such diseases, but also for growth promotion. Consequently, these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans, animals, and the environment. To break down the antimicrobial resistance (AMR), poultry producers are restricting the antimicrobial use (AMU) while adopting the antibiotic-free (ABF) and organic production practices to satisfy consumers’ demands. However, it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome. Various Gram-negative (Salmonella enterica serovars, Campylobacter jejuni/coli, E. coli) and Gram-positive (Enterococcus spp., Staphylococcus spp. and C. perfringens) bacteria harboring multiple AMR determinants have been reported in poultry including organically- and ABF-raised chickens. In this review, we discussed major poultry production systems (conventional, ABF and organic) and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportunities to develop efficient and safe production practices in controlling pathogens.
RETRACTED ARTICLE: Embelin alleviates weaned
piglets intestinal inflammation and barrier dysfunction via PCAF/NF-κB signaling pathway
in intestinal epithelial cells
Authors: Yao Weilei , Wang Tongxin , Huang Lu , Bao Zhengxi , Wen Shu , Huang Feiruo 
Published: December 2022

Abstract
Background
Intestinal barrier plays key roles in maintaining intestinal
homeostasis. Inflammation damage can severely destroy the intestinal integrity
of mammals. This study was conducted to investigate the protective effects of
embelin and its molecular mechanisms on intestinal inflammation in a porcine
model. One hundred sixty 21-day-old castrated weaned pigs
(Duroc × Landrace × Yorkshire, average initial body weight was 7.05 ± 0.28 kg,
equal numbers of castrated males and females) were allotted to four groups and
fed with a basal diet or a basal diet containing 200, 400, or 600 mg embelin/kg
for 28 d. The growth performance, intestinal inflammatory cytokines, morphology
of jejunum and ileum, tight junctions in the intestinal mucosa of piglets were
tested. IPEC-1 cells with overexpression of P300/CBP associating factor (PCAF)
were treated with embelin, the activity of PCAF and acetylation of nuclear
factor-κB (NF-κB) were analyzed to determine the effect of embelin on PCAF/NF-κB
pathway in vitro.

Results
The results showed that embelin decreased (P < 0.05) serum D-lactate
and diamine oxidase (DAO) levels, and enhanced the expression of ZO-1, occludin
and claudin-1 protein in jejunum and ileum. Moreover, the expression levels of
critical inflammation molecules (interleukin-1β, interleukin-6, tumor necrosis
factor-α, and NF-κB) were down-regulated (P < 0.05) by embelin in jejunal and ileal mucosa. Meanwhile, the
activity of PCAF were down-regulated (P < 0.05) by embelin. Importantly, transfection of PCAF siRNAs to
IPEC-1 cell decreased NF-κB activities; embelin treatment downregulated
(P < 0.05) the acetylation and
activities of NF-κB by 31.7%–74.6% in IPEC-1 cells with overexpression of
PCAF.

Conclusions
These results suggested that embelin ameliorates intestinal
inflammation in weaned pigs, which might be mediated by suppressing the
PCAF/NF-κB signaling pathway.
Epidemiological survey and genetic characterization of type 3 vaccine-derived poliovirus isolated from a patient with four doses of inactivated polio vaccine in Henan Province, China
Authors: Zhang Mingyu , Yang Jianhui , Bai Yiran , Zhu Hui , Wang Changshuang , Zhang Lu , Xu Jin , Lu Mingxia , Zhang Xiaoxiao , Xiao Zhanpei , Ma Yating , Wang Yan , Li Xiaolei , Wang Dongyan , Zhu Shuangli , Yan Dongmei , Xu Wenbo , Zhang Yong , Zhang Yanyang 
Published: December 2022

Abstract
Background
Vaccine-derived poliovirus (VDPV) is a potential threat to polio eradication because they can reintroduce into the general population and cause paralytic polio outbreaks, a phenomenon that has recently emerged as a prominent public health concern at the end of global polio eradication. This study aimed to describe the epidemiology and genetic characteristics of the first VDPV identified from a patient with acute flaccid paralysis (AFP), with four doses of inactivated polio vaccine immunization in Henan Province, China in 2017.

Methods
The patient was diagnosed with type 3 VDPV. Subsequently, a series of epidemiological approaches was implemented, including a retrospective search of AFP cases, rate of vaccination assessment, study of contacts, and supplementary immunization activities. Fecal samples were collected, viral isolation was performed, and the viral isolates were characterized using full-length genomic sequencing and bioinformatic analysis.

Results
Phylogenetic analysis showed that the viral isolates from the patient were different from other reported genetic clusters of type 3 VDPV worldwide. They were identified as a Sabin 3/Sabin 1 recombinant VDPV with a crossover site in the P2 region. Nucleotide substitutions, including U → C (472) and C → U (2493), have been identified, both of which are frequently observed as reversion mutations in neurovirulent type 3 poliovirus. A unique aspect of this case is that the patient had been vaccinated with four doses of inactive polio vaccine, and the serum neutralizing antibody for Sabin types 1 and 3 were 1∶16 and 1∶512, respectively. Thus, the patient was speculated to have been infected with type 3 VDPV, and the virus continued to replicate and be excreted for at least 41 d.

Conclusions
The existence of this kind of virus in human population is a serious risk and poses a severe challenge in maintaining a polio-free status in China. To the best of our knowledge, this is the first report of VDPV identified in the Henan province of China. Our results highlight the importance of maintaining a high-level vaccination rate and highly sensitive AFP case surveillance system in intercepting VDPV transmission.
Using a grid-search approach to validate the Graves–Pitarka broadband simulation method
Authors: Graves Robert 
Published: December 2022

AbstractThis work assesses the ability of the Graves–Pitarka simulation approach to reproduce observed ground motions for 12 California and Baja California earthquakes. A total of 240 realizations are computed for each earthquake and compared with recorded strong motions from near-fault sites. In addition to spatial variability in slip, each realization samples from discrete combinations of average rupture speed, rise time, and down-dip fault width. Ground motions for each realization of a given earthquake are compared to the observations using a pseudo-spectral acceleration goodness-of-fit (GoF) metric. Parameters for the lowest misfit cases are then tabulated to develop relations for estimating median values and ranges for future applications. The results are generally consistent with published scaling relations for estimating rupture dimensions as a function of magnitude. Additionally, I find the average rise time scales as $${2.3\times \alpha }_{T}\times {10}^{-9}{\times M}_{o}^{1/3}$$

2.3
×
α

T

×

10

-
9

×
M

o

1
/
3

(Mo is seismic moment in dyne-cm) and average rupture speed as $$(0.765 \pm 0.075)\times {\alpha }_{T}^{-1}\times {V}_{s}$$

(
0.765
±
0.075
)

×

α

T

-
1

×

V
s

(Vs is local shear wave velocity), where aT is a mechanism adjustment ranging from a value of 1.0 for pure strike-slip to 0.9 for pure reverse-slip cases. There are cases where slightly different combinations of parameters produce equally good fits to the observations, demonstrating the non-uniqueness of using a single GoF metric in this approach. Nonetheless, the results reinforce the importance of adequately sampling ranges of rupture parameters when performing validations, as well as when simulating ground motions for future events.
Graphical Abstract