bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nano2NGS-Muta: a framework for converting nanopore sequencing data to NGS-liked sequencing data for hotspot mutation detection
Authors: Lang Jidong , Sun Jiguo , Yang Zhi , He Lei , He Yu , Chen Yanmei , Huang Lei , Li Ping , Li Jialin , Qin Liu 
Published: April 2022

Abstract
Nanopore sequencing, also known as single-molecule real-time sequencing, is a third/fourth generation sequencing technology that enables deciphering single DNA/RNA molecules without the polymerase chain reaction. Although nanopore sequencing has made significant progress in scientific research and clinical practice, its application has been limited compared with next-generation sequencing (NGS) due to specific design principle and data characteristics, especially in hotspot mutation detection. Therefore, we developed Nano2NGS-Muta as a data analysis framework for hotspot mutation detection based on long reads from nanopore sequencing. Nano2NGS-Muta is characterized by applying nanopore sequencing data to NGS-liked data analysis pipelines. Long reads can be converted into short reads and then processed through existing NGS analysis pipelines in combination with statistical methods for hotspot mutation detection. Nano2NGS-Muta not only effectively avoids false positive/negative results caused by non-random errors and unexpected insertions-deletions (indels) of nanopore sequencing data, improves the detection accuracy of hotspot mutations compared to conventional nanopore sequencing data analysis algorithms but also breaks the barriers of data analysis methods between short-read sequencing and long-read sequencing. We hope Nano2NGS-Muta can serves as a reference method for nanopore sequencing data and promotes higher application scope of nanopore sequencing technology in scientific research and clinical practice.
Population-Based Assessment of Contact Tracing Operations for Coronavirus Disease 2019 in Pirkanmaa Hospital District, Finland
Authors: Rannikko Juha , Viskari Hanna , Sirkeoja Simo , Tamminen Pekka , Kaila Ville , Ala-Mursula Anni , Huttunen Reetta , Laine Janne , Syrjänen Jaana , Nuorti J Pekka 
Published: April 2022

Abstract

Background
The coronavirus disease 2019 (COVID-19) epidemic overwhelmed local contact tracing (CT) efforts in many countries. In Finland, severe acute respiratory syndrome coronavirus 2 incidence and mortality were among the lowest in Europe during 2020–2021. We evaluated CT efficiency, effectiveness, and transmission settings.

Methods
Polymerase chain reaction (PCR) test–positive COVID-19 cases and high-risk contacts in the population-based CT database of Pirkanmaa Hospital District (population 540 000) during June 2020–May 2021 were interviewed.

Results
Altogether 353 926 PCR tests yielded 4739 (1.3%) confirmed cases (average 14-day case notification rate, 34 per 100 000 population); about 99% of confirmed cases and high-risk contacts were reached by a CT team. Of 26 881 high-risk contacts who were placed in quarantine, 2275 subsequently tested positive (48% of new cases), 825 (17%) had been in quarantine ≥48 hours before symptoms, and 3469 (77%) of locally acquired cases were part of transmission chains with an identified setting. The highest secondary attack rates were seen in households (31%), healthcare patients (18%), and private functions (10%). Among the 311 hospitalized patients, COVID-19 diagnosis or exposure was known in 273 (88%) before emergency room admission (identified patients). Healthcare workers had the highest proportion of work-related infections (159 cases [35%]). The source of infection was classifiable in 65% and was most commonly a coworker (64 cases [62%]).

Conclusions
Our data demonstrate the role of effective testing and CT implementation during the cluster phase of COVID-19 spread. Although half of newly diagnosed cases were already in quarantine, targeted public health measures were needed to control transmission. CT effectiveness during widespread community transmission should be assessed.
TIPSS as a bridge to extrahepatic abdominal surgery: a case report
Authors: Kapeleris Audrey Pamela , Venkatachalapathy Suresh 
Published: April 2022

Abstract
Severe portal hypertension in cirrhosis is a relative contraindication to major surgical intervention. Pre-surgical placement of a transjugular intrahepatic portosystemic shunt (TIPSS) can potentially reduce portal hypertension and the risk of intraoperative bleeding. Two patients in our service, with cirrhosis and portal hypertension, required abdominal surgery and underwent TIPSS placement as a potential bridging therapy. Patient 1, a 56-year-old female, successfully underwent surgery with no intraoperative complications. Patient 2, a 36-year-old male, experienced liver decompensation post-TIPSS and is currently awaiting a liver and bowel transplant. Prophylactic TIPSS placement may allow some patients with decompensated cirrhosis to successfully undergo major extrahepatic abdominal surgery. However, careful patient selection and preoperative counselling for decompensation is necessary.
Giant hydronephrosis secondary to an ectopic ureter associated with bilateral duplex collecting system: a case report
Authors: Muhamad Muhamad Sinan , Mousa Mohammad Anas , Oukan Majdy , Razzok Ali 
Published: April 2022

Abstract
Giant hydronephrosis is an ultimate rare urologic entity; even rarer when it is secondary to a duplex collecting system. Duplex collecting system is a common urologic anomaly with a wide range of clinical symptoms and a variety of associated urologic abnormalities such as an ectopic ureter, ureterocele, vesicoureteral reflux and ureteropelvic junction obstruction. This report presents a case of an 8-year-old boy who had a bilateral duplex collecting system that was revealed accidentally by a bilateral severe hydronephrosis. The duplication was complete on the left side and partial on the right with a right ectopic ureteral orifice, in addition to a bilateral vesicoureteral reflux. The vesicoureteral reflux retreated completely in the left side after using a urethral catheter for 6 months, while the decision of performing a surgical operation for the right side was made.
Sacral osteomyelitis as a rare cause of anorectal pain several years following treatment for rectal carcinoma
Authors: Fernandes Darren C R , Srinivasan Sangeetha , Andreyev Hubert Jervoise N 
Published: April 2022

Abstract
A 66-year-old man was treated for a moderately differentiated T3 N1 M0 adenocarcinoma of the rectum in 2015 with preoperative short course radiotherapy, anterior resection and then adjuvant chemotherapy with oxaliplatin and capecitabine. Following ileostomy reversal, he complained of intense, unremitting anorectal pain. After repeated scans, computed tomography (CT) showed findings suggestive of a longstanding anastomotic leak. Subsequent, magnetic resonance imaging (MRI) revealed osteomyelitis of the sacrum, with the development of sacral osteomyelitis in this context unusual. Our case highlights the importance of appropriate radiological imaging and that clinicians should consider osteomyelitis as a differential diagnosis in patients presenting with severe anorectal pain after treatment for rectal cancer.
A case of tongue cancer manifesting from oral leukoplakia after long-term administration of pegylated liposomal doxorubicin
Authors: Nishimura Mai , Nomura Hidetaka , Omi Makiko , Netsu Sachiho , Sato Yukiko , Kanao Hiroyuki 
Published: April 2022

Abstract
We present a case of tongue cancer manifestation from oral leukoplakia after administration of pegylated liposomal doxorubicin (PLD). A 56-year-old woman was diagnosed with ovarian cancer. After preoperative chemotherapy with paclitaxel and carboplatin (TC), she underwent interval debulking surgery. Five cycles of TC therapy were carried out as adjuvant chemotherapy; however, recurrence was observed. Despite administration of gemcitabine-carboplatin therapy, the patient’s condition was judged as advancing to a progressive disease. PLD treatment was completed at a total dose of 1140 mg/m2. Two months after the end of treatment, the patient was diagnosed with leukoplakia. The leukoplakia lesion became thicker at each 3-month follow-up. She was diagnosed with tongue cancer and underwent a partial resection 2 years and 3 months after the completion of PLD treatment. Our report suggests that the risk of malignant transformation to tongue cancer persists even after the completion of treatment with PLD.
Sintilimab in Patients with Previously Treated Metastatic Neuroendocrine Neoplasms
Authors: Jia Ru , Li Yi , Xu Nong , Jiang Hai-Ping , Zhao Chuan-Hua , Liu Rong-Rui , Shi Yue , Zhang Yao-Yue , Wang Shu-Yan , Zhou Hui , Xu Jian-Ming 
Published: April 2022

Abstract

Background
Neuroendocrine neoplasms (NENs) are a group of diseases that show high heterogeneity but have limited treatment options. This phase I study evaluated the safety and efficacy of sintilimab, anti-PD-1 monoclonal antibody, in treating advanced NENs.

Methods
We prospectively enrolled patients pathologically diagnosed with NENs after standard treatment failure. Neuroendocrine neoplasms were classified into well-differentiated neuroendocrine tumors (NETs) and poorly differentiated neuroendocrine cancers (NECs). Every patient received sintilimab, and response was assessed every 9 weeks.

Results
Twenty-four patients with a median age of 57.0 years were enrolled from November 2016 to 2017. The median Ki-67 index was 60%. Five patients had NET, 1 had NET G3, 17 had NEC, and 1 had mixed adenocarcinoma-neuroendocrine carcinoma. The most common primary tumor sites were the pancreas and gastrointestinal tract in 7 and 10 patients, respectively. In phase Ia trial, 2 patients received sintilimab 1 mg/kg every 2 weeks, one received 3 mg/kg every 2 weeks, and 21 patients enrolled in the phase Ib trial received 200 mg every 3 weeks. The objective response rate was 20.8% in all enrolled patients and 27.8% in NEC patients. The median progression-free survival was 2.2 and 2.1 months in patients with NET and NEC, respectively. The median OS was not applicable (NA) and 10.8 months (95% CI, 4.3, NA) with NET and NEC, respectively. The duration of response (DOR) was not reached, with a median follow-up time of 20.7 months. Treatment-related adverse events (TRAE) occurred in 17 (70.8%) patients. The most frequent TRAE was thyroid dysfunction (41.7%), and a grade 3 pulmonary infection occurred in 1 patient. The programmed cell death 1-ligand 1 (PD-L1)-positive (tumor proportion score ≥1%) rate was 18.8% (3 out of 16) and the expression of PD-L1 did not correlate with response.

Conclusion
Sintilimab was well-tolerated and showed encouraging response in NECs.

ClinicalTrials.gov Identifier
NCT02937116.
Designing of small organic non-fullerene (NFAs) acceptor molecules with an A−D−A framework for high-performance organic solar cells: A DFT and TD-DFT method
Authors: Numbury Surendra Babu 
Published: April 2022

Abstract
The main objective of this research was to design non-fullerene acceptors (NFAs) A–D–A framework, using carbazole and benzothiazole derivatives. Density functional theory (DFT) was used to calculate the geometry optimized structures and electronic properties at B3LYP functional with a 6-311G basis set in the gas and solvent phase. The frontier molecular orbitals (FMO), bandgap, open-circuit voltage (VOC) and dipole moments of these developed acceptors have been calculated. The theoretical UV absorption spectra were calculated from time-dependent DFT with the same level of theory used DFT method. They show a suitable bandgap (2.24–2.93 eV) and dipole moment (1.8–10.8 Debye). The maximum wavelength (λmax) for all studied molecules in the range is 665.17–679.97 in both gas and solvent. A slight redshift was observed in all acceptors selected for chlorobenzene compared with gas phase absorption. The NFA A11 has the lowest bandgap energy (2.24 eV), gas-phase excitation energy (1.86 eV) and chlorobenzene excitation energy (1.86 eV). As a result, A11 is predicted to be a good contender for organic NFAs in the future. The open-circuit voltage (VOC) values range from 1.53 to 2.56 eV. Consequently, the optoelectronic, molecular orbital distribution and A11 and A12 molecules were suitable acceptors for NFAs.
Women and the Fight for Urban Change in Late Francoist Spain
Authors: Webster Roseanna 
Published: April 2022

Abstract
This article explores how Spanish women formed grassroots groups to fight for the transformation of their neighbourhoods in the late 1950s and 1960s — the latter years of Francisco Franco’s dictatorship. In contrast to most histories of feminism, which focus on literate, secular groups in universities or the centres of cities, its subjects are activists based on the outskirts of Madrid and in the industrial areas of Asturias, many of whom were Catholic, came from rural areas and left school before the age of 14.
Histories of feminism have tended to overlook completely movements in the southern European dictatorships, while accounts of modern Spain often see male politicians and experts as the driving forces shaping the built environment under Franco. But photographs, archival material and oral history interviews show that women demanded ‘cosas básicas’ (basic resources) on a widespread scale in Asturias and Madrid. They made these claims in the context of unprecedented internal migration, industrial unrest and the spread of social Catholic movements: factors often neglected in studies of social movements. The women involved have sometimes struggled, however, to take pride in their actions in later life. Patterns in their life stories suggest why, and offer insight into what agitating under Franco has meant for how they understand their lives, identities and relationships.
SMAX1 potentiates phytochrome B-mediated hypocotyl thermomorphogenesis
Authors: Park Young-Joon , Kim Jae Young , Park Chung-Mo 
Published: April 2022

Abstract
Plant thermosensors help optimize plant development and architecture for ambient temperatures, and morphogenic adaptation to warm temperatures has been extensively studied in recent years. Phytochrome B (phyB)-mediated thermosensing and the gene regulatory networks governing thermomorphogenic responses are well understood at the molecular level. However, it is unknown how plants manage their responsiveness to fluctuating temperatures in inducing thermomorphogenic behaviors. Here, we demonstrate that SUPPRESSOR OF MAX2 1 (SMAX1), known as a karrikin signaling repressor, enhances the thermosensitivity of hypocotyl morphogenesis in Arabidopsis thaliana. Hypocotyl thermomorphogenesis was largely disrupted in SMAX1-deficient mutants. SMAX1 interacts with phyB to alleviate its suppressive effects on the transcription factor activity of PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), promoting hypocotyl thermomorphogenesis. Interestingly, the SMAX1 protein is slowly destabilized at warm temperatures, preventing hypocotyl overgrowth. Our findings indicate that the thermodynamic control of SMAX1 abundance serves as a molecular gatekeeper for phyB function in thermosensitizing PIF4-mediated hypocotyl morphogenesis.
Differential effects of an experimental model of prolonged sleep disturbance on inflammation in healthy females and males
Authors: Besedovsky Luciana , Dang Rammy , Engert Larissa C , Goldstein Michael R , Devine Jaime K , Bertisch Suzanne M , Mullington Janet M , Simpson Norah , Haack Monika 
Published: April 2022

Abstract
Sleep disturbances, including disrupted sleep and short sleep duration, are highly prevalent and are prospectively associated with an increased risk for various widespread diseases, including cardiometabolic, neurodegenerative, chronic pain, and autoimmune diseases. Systemic inflammation, which has been observed in populations experiencing sleep disturbances, may mechanistically link disturbed sleep with increased disease risks. To determine whether sleep disturbances are causally responsible for the inflammatory changes reported in population-based studies, we developed a 19-day in-hospital experimental model of prolonged sleep disturbance inducing disrupted and shortened sleep. The model included delayed sleep onset, frequent nighttime awakenings, and advanced sleep offset, interspersed with intermittent nights of undisturbed sleep. This pattern aimed at providing an ecologically highly valid experimental model of the typical sleep disturbances often reported in the general and patient populations. Unexpectedly, the experimental sleep disturbance model reduced several of the assessed proinflammatory markers, namely interleukin(IL)-6 production by monocytes and plasma levels of IL-6 and C-reactive protein (CRP), presumably due to intermittent increases in the counterinflammatory hormone cortisol. Striking sex differences were observed with females presenting a reduction in proinflammatory markers and males showing a predominantly proinflammatory response and reductions of cortisol levels. Our findings indicate that sleep disturbances causally dysregulate inflammatory pathways, with opposing effects in females and males. These results have the potential to advance our mechanistic understanding of the pronounced sexual dimorphism in the many diseases for which sleep disturbances are a risk factor.
The genomic prehistory of the Indigenous peoples of Uruguay
Authors: Lindo John , De La Rosa Rosseirys , Santos Andre L C d , Sans Mónica , DeGiorgio Michael , Figueiro Gonzalo 
Published: April 2022

Abstract
The prehistory of the people of Uruguay is greatly complicated by the dramatic and severe effects of European contact, as with most of the Americas. After the series of military campaigns that exterminated the last remnants of nomadic peoples, Uruguayan official history masked and diluted the former Indigenous ethnic diversity into the narrative of a singular people that all but died out. Here, we present the first whole genome sequences of the Indigenous people of the region before the arrival of Europeans, from an archaeological site in eastern Uruguay that dates from 2,000 years before present. We find a surprising connection to ancient individuals from Panama and eastern Brazil, but not to modern Amazonians. This result may be indicative of a migration route into South America that may have occurred along the Atlantic coast. We also find a distinct ancestry previously undetected in South America. Though this work begins to piece together some of the demographic nuance of the region, the sequencing of ancient individuals from across Uruguay is needed to better understand the ancient prehistory and genetic diversity that existed before European contact, thereby helping to rebuild the history of the Indigenous population of what is now Uruguay.
Association of insomnia and short sleep duration, alone or with comorbid obstructive sleep apnea, and the risk of chronic kidney disease
Authors: Beaudin Andrew E , Raneri Jill K , Ahmed Sofia , Hirsch Allen A J , Nocon Andrhea , Gomes Teresa , Gakwaya Simon , Sériès Frédéric , Kimoff John R , Skomro Robert , Ayas Najib , Hanly Patrick J 
Published: April 2022

Abstract

Study Objectives
Obstructive sleep apnea (OSA), sleep fragmentation, and short sleep duration (SD) have been associated with chronic kidney disease (CKD). However, these potential mechanisms for CKD have not been compared in the same cohort. This study investigated the independent and combined impact of OSA and insomnia with short sleep duration on the risk of CKD progression in a sleep clinic population.

Methods
In a cross-sectional study design, adults with suspected OSA completed an overnight sleep study and a questionnaire that included the Insomnia Severity Index (ISI) and Pittsburgh Sleep Quality Index (PSQI). They also provided blood and urine samples for measurement of the glomerular filtration rate and urine albumin:creatinine ratio, from which the risk of CKD progression was determined.

Results
Participants (n = 732, 41% female, 55 ± 13 years) were categorized into four groups: no/mild OSA without insomnia (NM-OSA, n = 203), insomnia with SD without OSA (Insomnia-SD, n = 104), moderate-to-severe OSA without insomnia (MS-OSA, n = 242), and comorbid insomnia and OSA with SD (COMISA-SD, n = 183). After stratification, 12.8% of NM-OSA, 15.4% of Insomnia-SD, 28.9% of MS-OSA, and 31.7% of the COMISA-SD participants had an increased risk of CKD progression. Compared to NM-OSA, the odds ratio (OR) for an increased risk of CKD progression was not increased in Insomnia-SD (OR 0.95, confidence interval [CI]: 0.45–1.99) and was increased to the same degree in MS-OSA (OR 2.79, CI: 1.60–4.85) and COMISA-SD (OR 3.04, CI: 1.69–5.47). However, the ORs were similar between the MS-OSA and COMISA-SD groups across all statistical models (p ≥ .883).

Conclusions
In a sleep clinic population, insomnia with short sleep duration does not increase the risk of CKD progression; nor does it further increase the risk of CKD progression associated with moderate-to-severe OSA.
Teaching Elementary School Students to Be Emergency Responders
Authors: Goedde Elizabeth , Combe Laurie G. , Bowlen Brandy , Kerry Bonnie 
Published: April 2022

ABSTRACT:
School nurses from the Klein Independent School District in Harris County, Texas, have educated students, some as young as kindergarteners, on cardiopulmonary resuscitation (CPR) and how to recognize and use automatic external defibrillators and provide basic first aid. Through a collaboration with community partners and CPR-certified high school students, these school nurses are empowering the next generation with lifesaving skills.
Improving ABCDEF Bundle Compliance and Clinical Outcomes in the ICU: Randomized Control Trial to Assess the Impact of Performance Measurement, Feedback, and Data Literacy Training
Authors: Brown Joan C. , Querubin Jynette A. , Ding Li , Mack Wendy J. , Chen-Chan Kai , Perez Fabiola , Barr Juliana , Peden Carol J. , Cobb J. Perren 
Published: April 2022

OBJECTIVES:
Describe the effects of data literacy training and continuous performance reports on ICU staff compliance with the 6-element ICU quality bundle approach known as the ABCDEF (A–F) bundle and patient outcomes.

DESIGN:
Stepped-wedge cluster randomized trial conducted during an institutional A–F bundle implementation program.

SETTING:
Single-center study conducted in eight adult ICUs.

PATIENTS:
Adult patients admitted for at least 24 hours, not undergoing active withdrawal of life support or palliative care.

INTERVENTIONS:
Four ICUs in the intervention group received bundle-related staff education, data literacy training, and weekly bundle performance reports during the 12-month study period. The four ICUs in the nonintervention group received none of these interventions. Bundle compliance and patient outcomes were tracked, including ICU and hospital mortality, transfer and discharge, discharge disposition, mechanical ventilation, and ICU delirium.

MEASUREMENT AND RESULTS:
In the intervention group, staff education alone increased bundle compliance from 9% to 16% (p < 0.0001); data literacy training further increased compliance from 16% to 21% (p = 0.03). This improvement was sustained throughout the study period including the onset of the COVID-19 pandemic and was greater than improvement in the nonintervention group (p < 0.001). Full A–F bundle compliance was associated with a lower likelihood of next-day ICU and hospital mortality, discharge to a facility other than home, and was associated with a higher likelihood of next-day extubation in patients. Next-day ICU and hospital discharge likelihood decreased, and delirium frequency was not affected.

CONCLUSIONS:
This is the first study demonstrating that the combination of staff education, data literacy training, and access to performance data improves A–F bundle compliance, sustains performance, and improves ICU patient outcomes (ICU and hospital mortality, mechanical ventilation duration, and home discharge rates). In contrast to previous studies, increased bundle compliance did not hasten ICU or hospital discharges or reduce delirium frequency in patients.