bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgical Reconstruction for Upper-Extremity Paralysis Following Acute Flaccid Myelitis
Authors: Doi Kazuteru , Sem Sei Haw , Hattori Yasunori , Sakamoto Sotetsu , Hayashi Kota , De la Red-Gallego Maria Angeles 
Published: October 2019

Background:
Acute flaccid myelitis (AFM) is a debilitating illness that is defined by the sudden onset of flaccid paralysis in the extremities with spinal magnetic resonance imaging (MRI) demonstrating a longitudinal lesion confined to the gray matter. The purpose of this study was to report the types of upper-extremity palsy and outcomes of surgical reconstruction in patients with AFM.

Methods:
Eight patients with a median age at onset of 3.8 years (range, 2.3 to 9.9 years) were identified. There was loss of shoulder abduction and external rotation in all patients, loss of elbow flexion in 5 patients, complete or partial loss of hand function in 3 patients, and spinal accessory nerve palsy in 2 patients. All patients underwent surgical reconstruction, which was categorized into 3 main groups: nerve transfer, secondary muscle transfer, and free muscle transfer.

Results:
The median follow-up period was 39 months (range, 30 to 94 months). Four patients obtained ≥90° of shoulder abduction whereas the other 4 patients had shoulder abduction of ≤70°. The 5 patients who received free muscle transfer or nerve transfer to restore elbow function obtained ≥140° of elbow flexion. Two patients treated with free muscle transfer to restore finger function obtained satisfactory total active motion of the fingers (180°).

Conclusions:
The patterns of paralysis and the strategy and outcomes of surgical reconstruction for patients with AFM differed from those for traumatic and obstetric brachial plexus palsy. All patients had loss of shoulder abduction, and 2 had spinal accessory nerve palsy. Restoration of shoulder function was unpredictable and depended on the quality of the donor nerves and recovery of synergistic muscles. Restoration of elbow and hand function was more consistent and satisfactory.

Level of Evidence:
Therapeutic Level IV. See Instructions for Authors for a complete list of levels of evidence.
Alkali/Cosolvent/Polymer Flooding of High-TAN Oil: Using Phase Experiments, Micromodels, and Corefloods for Injection-Agent Selection
Authors: Schumi Bettina , Clemens Torsten , Wegner Jonas , Ganzer Leonhard , Kaiser Anton , Hincapie Rafael E. , Leitenmüller Verena 
Published: October 2019

SummaryChemical enhanced oil recovery (EOR) leads to substantial incremental costs over waterflooding of oil reservoirs. Reservoirs containing oil with a high total acid number (TAN) could be produced by the injection of alkali. Alkali might lead to the generation of soaps and emulsify the oil. However, the generated emulsions are not always stable.Phase experiments are used to determine the initial amount of emulsions generated and their stability if measured over time. On the basis of the phase experiments, the minimum concentration of alkali can be determined and the concentration of alkali above which no significant increase in the formation of initial emulsions is observed.Micromodel experiments are performed to investigate the effects on the pore scale. For the injection of alkali into high-TAN oils, the mobilization of residual oil after waterflooding is seen. The oil mobilization results from the breaking up of oil ganglia or the movement of elongated ganglia through the porous medium. As the oil is depleting in surface-active components, residual oil saturation is left behind either as isolated ganglia or in the down gradient side of grains.Simultaneous injection of alkali and polymers leads to a higher incremental oil production in the micromodels owing to larger pressure drops over the oil ganglia and more-effective mobilization accordingly.Coreflood tests confirm the micromodel experiments, and additional data are derived from these tests. Alkali/cosolvent/polymer (ACP) injection leads to the highest incremental oil recovery of the chemical agents, which is difficult to differentiate in micromodel experiments. The polymer adsorption is substantially reduced if alkali is injected with polymers compared with polymer injection only. The reason is the effect of the pH on the polymers. As in the micromodels, the incremental oil recovery is also higher for alkali/polymer (AP) injection than with alkali injection only.To evaluate the incremental operating costs of the chemical agents, equivalent utility factors (EqUFs) are calculated. The EqUF takes the costs of the various chemicals into account. The lowest EqUF and, hence, the lowest chemical incremental operating expenditures are incurred by the injection of Na2CO3; however, the highest incremental recovery factor is seen with ACP injection. It should be noted that the incremental oil recovery owing to macroscopic-sweep-efficiency improvement by the polymer needs to be accounted for to assess the efficiency of the chemical agents.
Diagnostic evaluation of IgM ELISA and IgM Immunofluorescence assay for the diagnosis of Acute Scrub Typhus in central Nepal
Authors: Gautam Rajendra , Parajuli Keshab , Tshokey Tshokey , Stenos John , Sherchand Jeevan Bahadur 
Published: October 2019

Abstract
Introduction Scrub typhus is an acute febrile illness caused by the obligate intracellular bacterium,Orientia tsutsugamushi. Given their affordability and ease of use, antibody based diagnostic assays can be important diagnostic tools for early detection of scrub typhus fever in resource poor countries like Nepal. Immunochromatography (ICT) and IgM ELISA are two of the routinely employed antibody based assays for diagnosis of Scrub typhus fever in Nepal, although the recommended gold standard diagnostic test is IgM Immunofluorescence assay (IFA). This study evaluated the InBios Scrub Typhus Detect™ Immunoglobulin M (IgM) ELISA and IgM Immunofluorescence assays in single serum sample at the time of admission. Methodology Study participants (1585 suspected cases), were enrolled based on acute febrile illness with suspected scrub typhus cases in central Nepal from April 2017 to March 2018. Blood sample was collected from the suspected patients of scrub typhus, presenting with acute febrile illness. IgM antibody to Orientia tsusugamushi was detected by using Scrub Typhus Detect™ Kit (In Bios International, USA) and an in-house IgM IFA (Australian Rickettsial Reference Laboratory, Geelong, Australia. The IFA assay was performed with the Gilliam, Karp, Kato strains and O. chuto antigens following the ARRL protocol. Result Statistical analysis of ELISA IgM results when compared to reference test, IgM IFA results demonstrated the following characteristics, sensitivity 84.0% (95%CI: 79.73%-87.68%), specificity 94.82% (95% CI: 93.43%-95.99%), positive likelihood ratio 16.21% (95% CI: 12.71%-20.67%), negative likelihood ratio 0.17% (95% CI: 0.13-0.21%), disease prevalence 22.08% (95% CI: 20.06%-24.21%), positive predictive value 82.12% (95% CI: 78.28-85.42%) and negative predictive value 95.44% (95% CI: 94.27%-96.38%) respectively. Conclusion The study indicated that the IgM ELISA has the sensitivity 84.0% (95% CI: 79.73%-87.68%) and specificity 94.82% (95% CI: 93.43%-95.99%). Although IgM IFA is considered the gold standard test for the diagnosis of scrub typhus cases, it is relatively expensive, requires trained personal and a microscope with fluorescence filters. Scrub typhus IgM ELISA with appropriate OD cut–off values may be the best alternative test and possible viable option for resource limited endemic countries like Nepal.
Occurrence and seasonal variation of human Plasmodium infection in Punjab Province, Pakistan
Authors: Qureshi Naveeda Akhtar , Fatima Huma - , Afzal Muhammad , Khattak Aamer Ali , Nawaz Muhammad Ali 
Published: October 2019

Abstract
Background: Malaria is the fifth leading cause of death worldwide. Pakistan is considered as a moderate malaria-endemic country but still, 177 million individuals are at risk of malaria. Roughly 60% of Pakistan’s population, live in malaria-endemic regions. The present study is based upon the survey of various health care centers in 10 major cities of Northern and Southern Punjab to find out the malarial infection patterns in 2015. The diagnosis, seasonal variations, age and gender-wise distribution of Plasmodium spp. circulating in the study area were also included in the objectives.
Methods: The malaria-suspected patients ‘16075’ were enrolled for malaria diagnosis using microscopy, out of which 925 were malaria positive which were processed for molecular analysis using nested PCR. The 18S rRNA genes of Plasmodium species were amplified, sequenced, blast and the phylogenetic tree was constructed based on sequences using online integrated tool MEGA7.
Results: The 364 cases recruited from Northern Punjab with the highest incidence in Rawalpindi (25.5%) and lowest in Chakwal (15.9%). From Southern Punjab 561 cases were enlisted Rajanpur (21.4%) maximum and lowest from Multan and Rahim Yar Khan (18%). The slide positivity rate, annual parasite incidence, and annual blood examination rates were 5.7 per 1000 population, 0.1%, and 0.2% respectively. The only P. vivax (66.7%), P. falciparum (23.7%) and mixed infection by these two species (9.6%) were diagnosed. The same trend (P. vivax>P. falciparum > mixed infection) in species identification %age was confirmed from molecular analysis. However, the occurrence of malaria was higher in Southern Punjab (5.5%) as compared to the Northern Punjab (4.0%). The overall malaria percentage occurrence of treatment-seeking patients in all recruited cities of Punjab was 4.9%. The age-group of 1-20 and males among genders were more affected by malaria. The comparison of different seasons showed that the malaria infection was at a peak in Summer and post-monsoon.
Conclusion: The incidence of malaria was high in the flood infected rural areas of Southern Punjab, Summer, and post-monsoon. The age group (1-20) and gender-wise males were more affected by malaria.
A changing profile of infective endocarditis at a tertiary hospital in China: A retrospective study from 2001 to 2018
Authors: Ren Zuning , Mo Xichao , Chen Hongjie , Peng Jie 
Published: October 2019

Abstract
Background: Infective endocarditis (IE) is a lethal disease which has been changing significantly over the past decades; however, information about IE in China remains scarce. This study surveyed the changes in clinical characteristics of IE at a tertiary hospital in southern China over a period of nearly eighteen years. Methods: Medical records with IE patients consecutively hospitalized between June 2001 and June 2018 were selected from the electronic medical records system in Nanfang Hospital of Southern Medical University. Data were divided by admission time into two groups: early-period group, June 2001 to December 2009 and later-period group, January 2010 to July 2018. Results: A Total of 313 IE patients were included in our study. Compared with the early-period group, patients in the later-period group included fewer intravenous drug users (IVDU), older age at onset, reduced development of pulmonary embolism, less renal dysfunction, decreased proportion of Staphylococcus aureus infection and fewer vegetations observed in the right heart by echocardiography. The later-period group also showed a higher proportion of ischemic strokes and higher rate of whole-blood culture positive compared with the early-period group. The in-hospital mortality rate remained about the same between the two periods. Conclusions: Our study demonstrated a dramatic change in the profile and characteristics of IE over a period of eighteen years at a tertiary hospital in southern China, especially the decrease in intravenous drug users (IVDU), which might be responsible for many other changes.
Incidence and predictors of tuberculosis among HIV-positive adults on antiretroviral therapy at Debre Markos Referral Hospital, Northwest Ethiopia: A retrospective record review
Authors: Temesgen Belisty , Kibret Getiye Dejenu , Alamirew Nakachew Mekonnen , Melkamu Mamaru Wubale , Hibstie Yitbarek Tenaw , Petrucka Pammla , Alebel Animut 
Published: October 2019

Abstract
Background: Tuberculosis is the leading cause of morbidity and mortality among people living with human immunodeficiency virus. Almost one-third of deaths among people living with human immunodeficiency virus are attributed to tuberculosis. Despite this evidence, in Ethiopia, there is a scarcity of information regarding the incidence and predictors of tuberculosis among people living with HIV. Thus, this study assessed the incidence and predictors of tuberculosis among HIV-positive adults on antiretroviral therapy.
Methods: This study was a retrospective record review including 544 HIV-positive adults on antiretroviral therapy at Debre Markos Referral Hospital between January 1, 2012 and December 31, 2017. The study participants were selected using a simple random sampling technique. The data extraction format was adapted from antiretroviral intake and follow-up forms. Cox-proportional hazards regression model was fitted and Cox-Snell residual test was used to assess the goodness of fit. Tuberculosis free survival time was estimated using the Kaplan-Meier survival curve. Both the bi-variable and multivariable Cox-proportional hazard regression models were used to identify predictors of tuberculosis.
Results: In the final analysis, a total of 492 HIV-positive adults were included, of whom, 83 (16.9%) developed tuberculosis at the time of follow-up. This study found that the incidence of tuberculosis was 6.5 (95% CI: 5.2, 8.0) per 100-person-years (PY) of observation. Advanced World Health Organization clinical disease stage (III and IV) (AHR: 2.1, 95% CI: 1.2, 3.2), being ambulatory and bedridden (AHR: 1.8, 95% CI: 1.1, 3.1), baseline opportunistic infections (AHR: 2.8, 95% CI: 1.7, 4.4), low hemoglobin level (AHR: 3.5, 95% CI: 2.1, 5.8), and not taking Isonized Preventive Therapy (AHR: 3.9, 95% CI: 1.9, 7.6) were found to be the predictors of tuberculosis.
Conclusion: The study found that there was a high rate of tuberculosis occurrence as compared to previous studies. Baseline opportunistic infections, being ambulatory and bedridden, advanced disease stage, low hemoglobin level, and not taking Isonized Preventive Therapy were found to be the predictors of tuberculosis. Therefore, early detection and treatment of opportunistic infections like tuberculosis should get a special attention.
Keywords: Debre Markos, HIV, Incidence, Predictors, tuberculosis
Rapid identification and characterization of genetic loci for defective kernel in bread wheat
Authors: Fu Chao , Du Jiuyuan , Tian Xiuling , He Zhonghu , Fu Luping , Wang Yue , Xu Dengan , Xu Xiaoting , Xia Xianchun , Zhang Yan , Cao Shuanghe 
Published: October 2019

Abstract
Background Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential. Results Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78 - 18.17%, 16.61 - 21.83% and 19.08 - 28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were determined according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0. Conclusions Overall, we achieved a rapid QTL mapping and reasonable predication of causal genes for Dek, laying foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat.
Validating surgical procedure codes for inflammatory bowel disease in the Swedish National Patient Register
Authors: Forss Anders , Myrelid Pär , Olén Ola , Everhov Åsa H , Nordenvall Caroline , Halfvarson Jonas , Ludvigsson Jonas F. 
Published: October 2019

Abstract
Validating surgical procedure codes for inflammatory bowel disease in the Swedish National Patient Register Background: About 50% of patients with Crohn’s disease (CD) and about 20% of those with ulcerative colitis (UC) undergo surgery at some point during the course of the disease. The diagnostic validity of the Swedish National Patient Register (NPR) has previously been shown to be high for inflammatory bowel disease (IBD), but there are little data on the validity of IBD-related surgical procedure codes. Methods: Using patient chart data as the gold standard, surgical procedure codes registered between 1966 and 2014 in the NPR were abstracted and validated in 262 patients with a medical diagnosis of IBD. Of these, 53 patients had reliable data about IBD-related surgery. The positive predictive value (PPV), sensitivity and specificity of the surgical procedure codes were calculated. Results: In total, 158 codes were registered in the NPR. 155 of these, representing 60 different surgical procedure codes, were also present in the patient charts and validated using a standardized form. Of the validated codes 153/155 were concordant against the patient charts, corresponding to a PPV of 96.8% (95%CI=93.9-99.1). Stratified in abdominal, perianal and other surgery, the corresponding PPVs were 94.1% (95%CI=88.7-98.6), 100% (95%CI=100-100) and 98.1% (95%CI=93.1-100), respectively. Of 164 surgical procedure codes in the validated patient charts, 155 were registered in the NPR, corresponding to a sensitivity of the surgical procedure codes of 94.5% (95%CI=89.6-99.3). The specificity of the NPR was 98.5% (95%CI=97.6-100). Conclusions: Data on IBD-related surgical procedure codes are reliable, with the Swedish National Patient Register showing a high sensitivity and specificity for such surgery. Keywords: Epidemiology, Inflammatory bowel disease, Validation, National Patient Register, Procedure code
Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts
Authors: Garfoot Andrew , Wilson Gary , Coon Joshua , Knoll Laura 
Published: October 2019

Abstract
Background : The protozoan pathogen Toxoplasma gondii has the unique ability to develop a chronic infection in the brain of its host by transitioning from the fast growing tachyzoite morphology to latent bradyzoite morphology. A hallmark of the bradyzoite is the development of neuronal cysts that are resilient against host immune response and current therapeutics. The bradyzoite parasites within the cyst have a carbohydrate and protein-rich wall and a slow-replication cycle, allowing them to remain hidden from the host. The intracellular, encysted lifestyle of T. gondii has made them recalcitrant to molecular analysis in vivo .

Results : Here, we detail the results from transcriptional and proteomic analyses of bradyzoite-enriched fractions isolated from mouse brains infected with T. gondii over a time course of 21 to 150 days. The enrichment procedure afforded consistent identification of over 2,000 parasitic peptides from the mixed-organism sample, representing 366 T. gondii proteins at 28, 90, and 120 day timepoints. Deep sequencing of transcripts expressed during these three timepoints revealed that a subpopulation of genes that are transcriptionally expressed at a high level. Approximately one-third of these transcripts are more enriched during bradyzoite conditions compared to tachyzoites and approximately half are expressed at similar levels during each phase. The T. gondii transcript which increased the most over the course of chronic infection, sporoAMA1, shows stage specific isoform expression of the gene.

Conclusions : We have expanded the transcriptional profile of in vivo bradyzoites to 120 days post-infection and provided the first in vivo proteomic profile of T. gondii bradyzoites. The RNA sequencing depth of in vivo bradyzoite T. gondii was over 250-fold greater than previous reports and allowed us to identify low level transcripts and a novel bradyzoite-specific isoform of sporoAMA1.
Effectiveness of steroids vs placebo in preventing upper airway obstruction after extubation in critically-ill children: rationale and design of a multicentric, double-blind, randomized study.
Authors: Manrique Gema , Laiseca Laura Butragueño , González Rafael , Rey Corsino , Martínez Zuriñe , Gil Javier , Rodriguez Antonio , Martínez Cecilia , Manrique Silvia , López-Herce Jesús 
Published: October 2019

Abstract
Background Post-extubation upper airway obstruction (UAO) is a frequent complication causing stridor and respiratory distress, which occasionally may require reintubation, thereby increasing morbidity and mortality rates. Contradictory results have been obtained in studies assessing the effectiveness of steroids in preventing post-extubation UAO, and the available evidence is limited. We designed a multicentric randomized, placebo-controlled study to explore the effectiveness of dexamethasone in preventing post-extubation UAO in children. Methods A multicentric, prospective, double-blind, randomized, placebo-controlled, phase IV clinical trial has been designed. The sample will include pediatric patients between 1 month and 16 years of age who have been intubated for more than 48 hours. Patients with airway disorders or who have received steroids within the last seven days will be excluded. Patients will be randomized to receive either placebo or a therapy with dexamethasone 0.25 mg/kg every 6 hours to be started 6-to-12 hours prior to extubation, to a total of four doses. Randomization will be performed at a 1:1 ratio. Follow-up of patients will be carried out for 48 h after extubation. The main objective of this study is to assess the reduction of UAO symptoms following extubation, as measured using the Taussig scale. Secondary objectives include assessing the decrease in the incidence of reintubation, evaluating the use of additional therapies for upper airway obstruction, and monitoring dexamethasone potential side effects. Discussion The results of this study will contribute to the existing evidence on prophylaxis for post-extubation airway obstruction.