bluuebunny/crossref_metadata_2025_split huggingface dataset:
Execution by lethal injection: Autopsy findings of pulmonary edema
Authors: Zivot Joel B. , Edgar Mark A. , Lubarsky David A. 
Published: August 2022

AbstractLethal injection is the common method of capital punishment in the United States (US), but problematic executions feed controversy centered on the 8th amendment of the US constitution that proscribes cruel punishment.1 However, the definition of cruelty is contentious, and lethal injection displays few signs of the hidden course of a potentially cruel death. Few survive and those who die cannot give witness. In this study, we reviewed autopsy reports of prisoners executed by intravenous midazolam (usually followed by a neuromuscular blocking agent and potassium chloride) or pentobarbital as a single drug. Autopsy reports for 43 inmates obtained from eight states were reviewed to identify any abnormal findings. Pulmonary edema (often fulminant with froth filling airways) emerged as a consistent and unexpected abnormality in 33/43 autopsies (76.74%), 23/28 midazolam executions (82.14%), and 10/15 (66.66%) pentobarbital executions. Injecting heavy overdoses of either acidic or basic solutions into the bloodstream may be directly toxic to pulmonary capillary endothelial cells. The injury manifests by the sudden escape of edema fluid into normally air-filled lungs, resulting in pulmonary edema. These findings explain witnessed respiratory distress during executions and increase concern about an inability of an execution witness to observe such a finding when a paralytic is added.
Death Registration coverage in India: Results from nationally representative survey
Authors: Saikia Nandita , Kumar Krishna , Das Bhaswati 
Published: August 2022

AbstractObjectiveTo investigate the disparity and predictors of death registration in India.MethodsWe used National Family Health Survey (NFHS-2019-21) data. Based on eligible household members’ reports, we estimated death registration coverage among 84,390 deaths in all age groups across the country. We did multilevel binary logistic regression to examine demographic and socio-demographic predictor variables of death registration at state, district, and individual levels. We used GIS software for spatial mapping of the level of death registration at the district level, disaggregated by sex.FindingsThe death registration at the national level is 71%. We found that out of 707 districts in 2019, 122 and 53 districts recorded death registration level below 40 percent among females and males, respectively. There was a considerable difference in the death registration level by sex (male-74% and female-66%). Death registration level was higher in urban areas compared to rural areas (83% vs. 66%). We found death registration level was higher among households with BPL cards (72%), bank accounts (71%) and covered with health insurance (77%). Females, rural populations, people from disadvantaged castes, poorest wealth quintile, Muslims, and not having BPL cards have a lower likelihood of death registration in India. District-level predictors were not statistically significant in the model.ConclusionDemographic and socioeconomic characteristics of the deceased are significantly associated with their death registration. We suggest periodic awareness programs on death registration procedures and facilitating easy access to death registration offices in lower performing districts and areas among the marginalised population groups.
Inflammation and cognition in severe mental illness: Patterns of covariation and subgroups
Authors: Sæther Linn Sofie , Ueland Thor , Haatveit Beathe , Maglanoc Luigi A. , Szabo Attila , Djurovic Srdjan , Aukrust Pål , Roelfs Daniel , Mohn Christine , Greenwood Ormerod Monica Bettina Elkjaer , Lagerberg Trine Vik , Steen Nils Eiel , Melle Ingrid , Andreassen Ole A. , Ueland Torill 
Published: August 2022

AbstractCognitive impairments are common in severe mental illnesses (SMI), such as schizophrenia (SZ) and bipolar (BD) spectrum disorders, with substantial heterogeneity in both diagnostic categories. It has been suggested that dysregulation of immune and inflammatory pathways may contribute to cognitive impairment. This study aimed to investigate covariance patterns between cognitive domains and inflammatory/immune-related markers and further elucidate inter-individual variance in a large SMI and healthy control (HC) cohort (SZ = 343, BD = 298, HC = 770). We applied canonical correlation analysis (CCA) to identify modes of maximum covariation between a comprehensive selection of cognitive measures and inflammatory/immune markers. We found that poor verbal learning and psychomotor processing speed was associated with higher levels of interleukin-18 system cytokines and beta defensin 2, reflecting enhanced activation of innate immunity, a pattern augmented in SMI compared to HC. Applying hierarchical clustering on covariance patterns identified by the CCA revealed a high cognition – low immune dysregulation subgroup with predominantly HC (24% SZ, 45% BD, 74% HC) and a low cognition – high immune dysregulation subgroup predominantly consisting of SMI patients (76% SZ, 55% BD, 26% HC). These subgroups differed in IQ, years of education, age, CRP, BMI (all groups), level of functioning, symptoms and DDD of antipsychotics (SMI cohort). Our findings suggest a potential link between cognitive functioning and innate immune dysregulation.
Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping
Authors: Nishimura Kazusa , Kokaji Hiroyuki , Motoki Ko , Yamazaki Akira , Nagasaka Kyoka , Takisawa Rihito , Yasui Yasuo , Kawai Takashi , Ushijima Koichiro , Yamasaki Masanori , Saito Hiroki , Nakano Ryohei , Nakazaki Tetsuya 
Published: August 2022

SummaryMultiplexed inter-simple sequence repeats genotyping by sequencing (MIG-seq) is an next-generation sequencing library construction method developed for the analysis of DNA in ecology. Although MIG-seq can generate libraries from low-quality DNA, few polymorphisms can be obtained in species with small genomes. In this study, we developed degenerate oligonucleotide primer MIG-seq (dpMIG-seq) as an effective polymorphism discovery method that allows for variation in the number of polymorphisms while retaining the advantages of MIG-seq, including independence from DNA quality. In dpMIG-seq, a proportion of the simple sequence repeats in the primer sequence of the first PCR in MIG-seq was changed to degenerate oligonucleotides to enable annealing to a wider range of sequences. In tests of several crop species other than wheat, the number of loci that could be sequenced using dpMIG-seq with a data volume of 0.3 gigabases (Gb) was increased compared with that sequenced using MIG-seq. In wheat, the number of polymorphisms obtained via dpMIG-seq was higher than that obtained via MIG-seq when a data volume of about ≥2 Gb was obtained. In dpMIG-seq, different loci could be sequenced by changing the positions of the degenerate oligonucleotides. By applying dpMIG-seq, we constructed a linkage map consisting of 5,142 markers for the rice inter-subspecies F2population, and we detected quantitative trait loci for heading date in the regions where known heading-related genes were located. Overall, our results show that dpMIG-seq is a useful tool for the genetic analysis of crop species.
Racial and Sociodemographic Disparities in Blindness Associated with Primary Angle Closure Glaucoma in the United States: An IRIS® Registry Analysis
Authors: Shah Sona N. , Zhou Sarah , Sanvicente Carina , Burkemper Bruce , Apolo Galo , Li Charles , Li Siying , Liu Lynn , Lum Flora , Moghimi Sasan , Xu Benjamin 
Published: August 2022

AbstractPurposeTo assess the prevalence and risk factors of blindness among patients newly diagnosed with primary angle closure glaucoma (PACG) in the United States (US).DesignRetrospective cross-sectional study of patients from the American Academy of Ophthalmology IRIS® (Intelligent Research in Sight) Registry.ParticipantsPatients in the IRIS® Registry between the years 2015 to 2019 with a new diagnosis of PACG and visual acuity (VA) data on or within 90 days prior to the date of diagnosis.MethodsEligible patients were aged 18 years and older and: (1) were observable in the database at least 24 months prior to the index date of PACG diagnosis; (2) had no history of intraocular pressure (IOP) lowering drops, laser peripheral iridotomy (LPI), cataract surgery, or a diagnosis of pseudophakia unless preceded by a diagnosis of anatomical narrow angle (ANA); and (3) had no history of glaucoma surgery. Multivariable logistic regression models were developed to assess risk factors of blindness.Main Outcome MeasuresAny (one or both eyes) or bilateral (both eyes) blindness (VA ≤ 20/200) at first diagnosis of PACG.Results43,901 patients with PACG in the IRIS® Registry met inclusion criteria. Overall prevalence of any and bilateral blindness were 11.5% and 1.8%, respectively. Black and Hispanic patients were at higher risk of any (OR=1.42 and 1.21, respectively; p<0.001) and bilateral (OR=2.04 and 1.53, respectively; p<0.001) blindness compared to non-Hispanic White patients adjusted for ocular comorbidities, including cataracts. Other factors associated with any blindness included age <50 or >80 years, male sex, Medicaid or Medicare insurance category, and Southern or Western practice region (ORs>1.28; p≤0.01). Diagnosis of ANA prior to diagnosis of PACG was protective against any (OR=0.56; p<0.001) and bilateral (OR=0.61; p<0.001) blindness.ConclusionsBlindness affects 1 out of 9 patients with newly diagnosed PACG in the IRIS® Registry; Black and Hispanic patients and Medicaid and Medicare recipients are significantly more vulnerable. These findings highlight the severe ocular morbidity associated with PACG and the need for increased disease awareness and improved detection methods.
Tracking neural correlates of prioritizing working memory representations through retrospective attentional strengthening
Authors: Li Dongwei , Hu Yiqing , Qi Mengdi , Zhao Chenguang , Jensen Ole , Huang Jing , Song Yan 
Published: August 2022

AbstractPrevious work has proposed two potentials benefits of retrospective attention on working memory (WM): target strengthening and non-target inhibition. It remains unknown which hypothesis contributes to the improved WM performance, yet the neural mechanisms responsible for this attentional benefit are unclear. Here, we recorded electroencephalography (EEG) signals while 33 participants performed a retrospective-cue WM task. Multivariate pattern classification analysis revealed that only representations of target features were enhanced by valid retrospective attention during the retention, supporting the target strengthening hypothesis. Further univariate analysis found that mid-frontal theta inter-trial phase coherence (ITPC) and ERP components were modulated by valid retrospective attention and correlated with individual differences and moment-to-moment fluctuations on behavioral outcomes, suggesting that both trait- and state-level variability in attentional preparatory processes influence goal-directed behavior. Furthermore, task-irrelevant target spatial location could be decoded from EEG signals, indicating that enhanced spatial binding of target representation promotes high WM precision. Importantly, frontoparietal theta-alpha phase-amplitude-coupling was increased by valid retrospective attention and predicted the reduced randomly guessing rates. This long-range connection supported top-down information flow in engagement of frontoparietal networks, which might organize attentional states to integrate target features. Altogether, these results provide neurophysiological bases that retrospective attention improves WM precision through enhancing representation of target and emphasize the critical role of frontoparietal attentional network in the control of WM representations.
Three-dimensional imaging of vascular development in the mouse epididymis: a prerequisite to better understand the post-testicular immune context of spermatozoa
Authors: Damon-Soubeyrand Christelle , Bongiovanni Antonino , Chorfa Areski , Goubely Chantal , Pirot Nelly , Pardanaud Luc , Pibouin-Fragner Laurence , Vachias Caroline , Bravard Stéphanie , Guiton Rachel , Thomas Jean-Léon , Saez Fabrice , Kocer Ayhan , Tardivel Meryem , Drevet Joël R. , Henry-Berger Joelle 
Published: August 2022

AbstractLong considered an accessory tubule of the male reproductive system, the epididymis is proving to be a key determinant of male fertility. In addition to its secretory role in ensuring functional maturation and survival of spermatozoa, the epididymis has a complex immune function. Indeed, it must manage both peripheral tolerance to sperm antigens foreign to the immune system and the protection of spermatozoa as well as the organ itself against pathogens ascending the epididymal tubule. Although our knowledge of the immunobiology of this organ is beginning to accumulate at the molecular and cellular levels, the organization of blood and lymphatic networks of this tissue, important players in the immune response, remains largely unknown. In the present report, we have taken advantage of a VEGFR3:YFP transgenic mouse model. Using high-resolution three-dimensional (3D) imaging and organ clearing coupled with multiplex immunodetections of lymphatic (LYVE1, PDPN, PROX1) and/or blood (PLVAP/Meca32) markers, we provide for the first time a simultaneous deep 3D view of the lymphatic and blood epididymal vasculature in the mature adult mouse as well as during postnatal development.Graphical abstractSummary of the expansion of the conventional and hybrid lymphatic vasculature during postnatal development of the murine epididymis.
Beyond linearity: Quantification of the mean for linear CRNs in a random environment
Authors: Sinzger-D’Angelo Mark , Startceva Sofia , Koeppl Heinz 
Published: August 2022

AbstractMolecular reactions within a cell are inherently stochastic, and cells often differ in morphological properties or interact with a heterogeneous environment. Consequently, cell populations exhibit heterogeneity both due to these intrinsic and extrinsic causes. Although state-of-the-art studies that focus on dissecting this heterogeneity use single-cell measurements, the bulk data that shows only the mean expression levels is still in routine use. The fingerprint of the heterogeneity is present also in bulk data, despite being hidden from direct measurement. In particular, this heterogeneity can affect the mean expression levels via bimolecular interactions with low-abundant environment species. We make this statement rigorous for the class of linear reaction systems that are embedded in a discrete state Markov environment. The analytic expression that we provide for the stationary mean depends on the reaction rate constants of the linear subsystem, as well as the generator and stationary distribution of the Markov environment. We demonstrate the effect of the environment on the stationary mean. Namely, we show how the heterogeneous case deviates from the quasi-steady state (Q.SS) case when the embedded system is fast compared to the environment.
The Impact of Task Context on Predicting Finger Movements in a Brain-Machine Interface
Authors: Mender Matthew J. , Nason-Tomaszewski Samuel R. , Temmar Hisham , Costello Joseph T. , Wallace Dylan M. , Willsey Matthew S. , Kumar Nishant Ganesh , Kung Theodore A. , Patil Parag G. , Chestek Cynthia A. 
Published: August 2022

ABSTRACTA key factor in the clinical translation of brain-machine interfaces (BMIs) for restoring hand motor function will be their robustness to changes in a task. With functional electrical stimulation (FES) for example, the patient’s own hand will be used to produce a wide range of forces in otherwise similar movements. To investigate the impact of task changes on BMI performance, we trained two rhesus macaques to control a virtual hand with their physical hand while we added springs to each finger group (index or middle-ring-small) or altered their wrist posture. Using simultaneously recorded intracortical neural activity, finger positions, and electromyography, we found that predicting finger kinematics and finger-related muscle activations across contexts led to significant increases in prediction error, especially for muscle activations. However, with respect to online BMI control of the virtual hand, changing either training task context or the hand’s physical context during online control had little effect on online performance. We explain this dichotomy by showing that the structure of neural population activity remained similar in new contexts, which could allow for fast adjustment online. Additionally, we found that neural activity shifted trajectories proportional to the required muscle activation in new contexts, possibly explaining biased kinematic predictions and suggesting a feature that could help predict different magnitude muscle activations while producing similar kinematics.
Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools
Authors: Steinberg Asher Preska , Silander Olin K. , Kussell Edo 
Published: August 2022

AbstractQuantifying SARS-like coronavirus (SL-CoV) evolution is critical to understanding the origins of SARS-CoV-2 and the molecular processes that could underlie future epidemic viruses. While genomic evidence implicates recombination as a factor in the emergence of SARS-CoV-2, few studies have quantified recombination rates among SL-CoVs. Here, we infer recombination rates of SL-CoVs from correlated substitutions in sequencing data using a coalescent model with recombination. Our computationally-efficient, non-phylogenetic method infers recombination parameters of both sampled sequences and the unsampled gene pools with which they recombine. We apply this approach to infer recombination parameters for a range of positive-sense RNA viruses. We then analyze a set of 191 SL-CoV sequences (including SARS-CoV-2) and find that ORF1ab and S genes frequently undergo recombination. We identify which SL-CoV sequence clusters have recombined with shared gene pools, and show that these pools have distinct structures and high recombination rates, with multiple recombination events occurring per synonymous substitution. We find that individual genes have recombined with different viral reservoirs. By decoupling contributions from mutation and recombination, we recover the phylogeny of non-recombined portions for many of these SL-CoVs, including the position of SARS-CoV-2 in this clonal phylogeny. Lastly, by analyzing 444,145 SARS-CoV-2 whole genome sequences, we show current diversity levels are insufficient to infer the within-population recombination rate of the virus since the pandemic began. Our work offers new methods for inferring recombination rates in RNA viruses with implications for understanding recombination in SARS-CoV-2 evolution and the structure of clonal relationships and gene pools shaping its origins.Significance StatementQuantifying the population genetics of SARS-like coronavirus (SL-CoV) evolution is vital to deciphering the origins of SARS-CoV-2 and pinpointing viruses with epidemic potential. While some Bayesian approaches can quantify recombination for these pathogens, the required simulations of recombination networks do not scale well with the massive amounts of sequences available in the genomics era. Our approach circumvents this by measuring correlated substitutions in sequences and fitting these data to a coalescent model with recombination. This allows us to analyze hundreds of thousands of sample sequences, and infer recombination rates for unsampled viral reservoirs. Our results provide insights into both the clonal relationships of sampled SL-CoV sequence clusters and the evolutionary dynamics of the gene pools with which they recombine.
Construction and rescue of a DNA-launched DENV2 16681 infectious clone
Authors: Holliday Madeline , Corliss Lochlain , Lennemann Nicholas J. 
Published: August 2022

ABSTRACTFlaviviruses represent a large group of globally significant, insect-borne pathogens. For many of these viruses, there is a lack of antivirals and vaccines. Thus, there is a need to continue the development of tools to further advance our efforts to combat these pathogens, including reverse genetics techniques. Traditionally, reverse genetics methods for flaviviruses rely on producing infectious RNA from in vitro transcription reactions followed by electroporation or transfection into permissive cell lines. However, production of Zika virus has been successful from CMV-promoter driven expression plasmids, which provides cost and time advantages. In this report, we describe the design and construction of a DNA-launched infectious clone for dengue virus (DENV) serotype 2 strain 16681. An artificial intron was introduced in the nonstructural protein 1 segment of the viral genome to promote stability in bacteria. We found that rescued virus maintained similar replication kinetics in several cell lines commonly used in flavivirus research. Thus, we present a rapid and cost-effective method for producing DENV2 strain 16681 from plasmid DNA. This construct will be a useful platform for the continued development of anti-DENV therapeutics and vaccines.
Neural oscillations in the aging brain associated with interference control in word production
Authors: Zheng Xiaochen Y. , Piai Vitória 
Published: August 2022

AbstractSpeaking is not only about retrieving words and structuring them into sentences, but it also requires top-down control to plan and execute speech. In previous electrophysiological research with young-adult speakers, mid-frontal theta oscillations have been observed using a picture-word interference paradigm. With this paradigm, participants name pictures while ignoring superimposed distractor words. In particular, mid-frontal theta power increases for categorically related distractors relative to other types of distractors, reflecting the top-down interference control in resolving the competition between processing streams during word production (Piai, Roelofs, Jensen, Schoffelen, & Bonnefond, 2014). In the present study, we conceptually replicated the magnetoencephalography study by Piai et al. (2014) with an older group of healthy adults (mean age of 60 years). Behaviorally, we replicated distractor semantic interference and Stroop-like interference effects usually observed in young adults. However, we did not find the corresponding theta modulation associated with these interference effects on the neural level. Instead, we found beta power decreases for both effects, mostly pronounced in the left posterior temporal and inferior parietal cortex. The distinct spectro-spatial-temporal profile of the oscillatory effects in the older population suggests different underlying dynamics relative to the midline frontal effect previously found in young-adult speakers. Our results indicate that the neural underpinnings of top-down interference control may be modified by aging, and that the mid-frontal theta cannot be the exclusive mechanism enabling interference control during spoken word production.