bluuebunny/crossref_metadata_2025_split huggingface dataset:
A deep neural network for high‐throughput measurement of functional traits on museum skeletal specimens
Authors: Weeks Brian C. , Zhou Zhizhuo , O'Brien Bruce K. , Darling Rachel , Dean Morgan , Dias Tiffany , Hassena Gemmechu , Zhang Mingyu , Fouhey David F. 
Published: April 2022

Abstract

Increasingly, natural history museum collections are being used to generate large‐scale morphological datasets to address a range of macroecological and macroevolutionary questions. One challenge to this approach is that large numbers of individuals either from a single species or from taxonomically broad sets of species may be necessary to characterize morphology at the relevant spatial, phylogenetic or temporal scales.

We present ‘Skelevision’, a method for rapidly handling, photographing and measuring skeletal specimens with a computer vision approach that uses a deep neural network to segment the photographs of specimens into individual bones, and identify and measure functional aspects of those bones.

We demonstrate the scale of what is feasible with Skelevision by estimating 11 functional traits from 11 different bones for 12,450 bird skeletal specimens spanning 1,882 species of passerines (~32% of all passerine diversity). We quantify the accuracy of Skelevision estimates by comparing them to handmade measurements for 174 specimens from 115 species across 79 genera that span 59 families. Skelevision is precise, with a mean standard deviation of 0.86 mm for repeated independent measurements of individual bones, and is extremely accurate, with a mean RMSE of 0.89 mm across all traits when compared to handmade measurements. There is minimal phylogenetic signal in the measurement error (mean Pagel's λ across traits = 0.13), and Skelevision estimates are robust to variation in the degree to which specimens remain articulated.

This approach has several important advantages over traditional methods for building large‐scale morphological datasets (e.g. measurements from long‐term field‐based operations or handmade measurements of museum specimens). First, measuring new specimens only requires the collection of photographs, which can then be measured automatically, and effectively instantaneously, with the neural network. This is a significant departure from the time and skill required to measure skeletal specimens by hand. Second, the measurements are repeatable. Third, even as the dataset of photographed specimens expands, the amount of annotation data needed to measure new traits on all of the photographed specimens using the neural network will remain fixed and can be done without re‐capturing images.
A comparison of multistep commodity price forecasts using direct and iterated smooth transition autoregressive methods
Authors: Ubilava David 
Published: April 2022

AbstractThe smooth transition autoregressive (STAR) modeling framework has gained popularity in commodity price analysis due to its ability to capture essential features of complex dynamics. This study addresses the questions of whether the improved in‐sample fit of STAR models results in more accurate forecasts compared to linear autoregressive models, and whether direct or iterated multistep STAR methods yield more accurate multistep forecasts. In the STAR framework, either a bootstrap simulation is necessary to numerically approximate iterated multistep forecasts, or a range of horizon‐specific STAR models needs to be estimated to generate direct multistep forecasts. The associated computational trade‐off underscores the need for a better understanding of advantages one method may have over another. Based on the analysis of 25 agricultural and nonagricultural commodity prices, this study finds that even when the STAR models appear to well approximate complex commodity price dynamics, they offer little advantage, and indeed, in most instances present as inferior alternatives to the basic autoregressive framework for multistep commodity price forecasting.
Exosome miR‐3184‐5p inhibits gastric cancer growth by targeting XBP1 to regulate the AKT, STAT3, and IRE1 signalling pathways
Authors: Lin Shuangming , Que Yonggu , Que Changrong , Li Fudi , Deng Maoqing , Xu Dongbo 
Published: April 2022

AbstractMicroRNAs can regulate the transcription of protein‐coding genes associated with the development and progression of cancer. In this study, we explored the potential diagnostic function of exosome miR‐3184‐5p in gastric cancer. This exosome was isolated from the blood samples of 150 patients with gastric cancer and 60 healthy participants. The mean particle size and concentration of serum exosome in the patients with gastric cancer were 104.6 nm (93.97–115.84) and 6.21e+009 particles/ml (5.15e+009–7.12e+009), respectively. miR‐3184‐5p expression was substantially downregulated in the patients with gastric cancer compared with that in the healthy participants. The gastric cancer cell line HGC‐27 was cultured and transfected with the mimic and an inhibitor to overexpress and inhibit miR‐3184‐5p expression. miR‐3184‐5p strongly suppressed cell proliferation, migration, and invasion but induced cell apoptosis. Luciferase reporter assay revealed that XBP1 was the target of miR‐3184‐5p. miR‐3184‐5p substantially downregulated the expression of CD44, cyclin D1, MMP2, p65, p‐AKT, and p‐STAT3 but upregulated that of GRP78, IRE1, p‐JNK, and CHOP. Moreover, miR‐3184‐5p cleaved caspase‐12 and inhibited BCL‐2 expression. These results suggested that the downregulation of miR‐3184‐5p in patients with gastric cancer might regulate the AKT, STAT3, and IRE1 pathways to promote the vitality of gastric cancer cells.
Clinical outcomes of treatment with idebenone in Leber's hereditary optic neuropathy in the Netherlands: A national cohort study
Authors: van Everdingen Judith A. M. , Pott Jan Willem R. , Bauer Noël J. C. , Krijnen Anna M. , Lushchyk Tanya , Wubbels René J. 
Published: April 2022

AbstractPurposeThe purpose of the study was to present results from a national Dutch cohort of patients with Leber's Hereditary Optic Neuropathy (LHON) treated with idebenone.MethodsThe multicentre, open‐label, retrospective evaluation of the long‐term outcome of idebenone treatment of Dutch LHON patients on visual function and on thickness of the retinal ganglion cell layer. Patients included in the analysis had a confirmed mutation in their mitochondrial DNA encoding either of the seven subunits of complex I, had a reported loss of vision in at least one eye and had a follow‐up of more than 6 months after their treatment was started. Control visits involved routine clinical examinations of visual function and retinal structure at (1) the start of treatment, (2) nadir (time of lowest visual acuity), (3) the time of recovery (if any), (4) the time of termination of treatment and (5) more than 6 months after termination of the treatment.ResultsData from 72 patients were analysed. Treatment duration was 23.8 ± 14.4 (mean ± SD) months. A positive response, that is either a clinically relevant recovery (CRR) or a clinically relevant stabilization (CRS), occurred in 53% and 11% of the patients, respectively. The magnitude of CRR was 0.41 ± 1.54 logMAR. CRR of visual acuity is associated with recovery of colour discrimination. The thickness of both the ganglion cell complex (GCC) and the retinal nerve fibre layer (RNFL) is irreversibly reduced.ConclusionOur results confirm that idebenone may help to restore or maintain visual function. Whether this effect will persist is still unknown. Thinning of retinal neural tissue appears to be permanent.
National cohort of infants born before 24 gestational weeks showed increased survival rates but no improvement in neonatal morbidity
Authors: Lundgren Pia , Morsing Eva , Hård Anna‐Lena , Rakow Alexander , Hellström‐Westas Lena , Jacobson Lena , Johnson Mats , Holmström Gerd , Nilsson Staffan , Smith Lois E. , Sävman Karin , Hellström Ann 
Published: April 2022

AbstractAimTo describe survival and neonatal morbidities in infants born before 24 weeks of gestation during a 12‐year period.MethodsData were retrieved from national registries and validated in medical files of infants born before 24 weeks of gestation 2007–2018 in Sweden. Temporal changes were evaluated.ResultsIn 2007–2018, 282 live births were recorded at 22 weeks and 460 at 23 weeks of gestation. Survival to discharge from hospital of infants born alive at 22 and 23 weeks increased from 20% to 38% (p = 0.006) and from 45% to 67% (p < 0.001) respectively. Caesarean section increased from 12% to 22% (p = 0.038) for infants born at 22 weeks. Neonatal morbidity rates in infants alive at 40 weeks of postmenstrual age (n = 399) were unchanged except for an increase in necrotising enterocolitis from 0 to 33% (p = 0.017) in infants born at 22 weeks of gestation. Bronchopulmonary dysplasia was more common in boys than girls, 90% versus 82% (p = 0.044). The number of infants surviving to 40 weeks doubled over time.ConclusionIncreased survival of infants born before 24 weeks of gestation resulted in increasing numbers of very immature infants with severe neonatal morbidities likely to have a negative impact on long‐term outcome.
Systematic ESG exposure and stock returns: Evidence from the United States during the 1991–2019 period
Authors: Karoui Aymen , Nguyen Duc Khuong 
Published: April 2022

AbstractUsing a sample of US stocks over the period 1991–2019, we test whether stocks with high exposure to a social index exhibit high returns. Using a univariate analysis, our in‐sample results show that stocks with high sensitivities to the MSCI KLD 400 Social Index underperform stocks with low sensitivities by an annual risk‐adjusted performance of 7.02%. The negative premium is also larger in the post‐crisis period of 2007–2019 and is equal to 10.25%. The out‐of‐sample results offer, however, only weak evidence of such a finding, with a risk‐adjusted performance difference of merely −0.84% over the full sample period and no significant differences between the pre‐crisis and post‐crisis periods. In the multivariate regression, we find evidence of a negative relationship between exposure to the social index and stock performance. Moreover, we find that stocks with high exposure to the social index display a low corporate social responsibility score, a high Tobin’s Q, high long‐term debt, a large size, high total risk, a high market beta, a high SMB coefficient, a low HML coefficient, and a small MOM coefficient.
In vitro effects of thirty‐eight cardiac drugs on human serum paraoxonase
Authors: Argan Onur , Cikrikci Kubra , Uslu Harun , Gencer Nahit 
Published: April 2022

AbstractIn this study, the effects of 38 commonly used cardiac drugs on the human paraoxonase (PON1) were investigated. PON1 was purified from human serum blood by ammonium sulfate precipitation (60%–80%) and hydrophobic interaction chromatography (Sepharose‐4B~L‐tyrosine~1‐napthylamine gel). All of the cardiac drugs inhibited PON1 at the micro molar level. IC50 and Ki values were determined for each drug. The tested drugs displayed potent PON1 inhibitory activity. It was found that the weakest PON1 inhibitors are Irbesartan (Ki: 421.73 µM), Glyceryl Trinitrate (Ki: 351.48 µM), and Apixaban (Ki: 333.27 µM). Bisoprolol hemifumarate (Ki: 269.31 µM) is also other weak PON1 inhibitor. Therefore, these drugs, having weak PON1 inhibitory activity, may be preferred primarily in patients with atheroclerotic heart disease compared to other drugs dueto the protective effect of PON1 on atherosclerosis. Conversely, the most potent inhibitors against PON1 were propafenone (Ki: 0.35 µM), Lacidipine (Ki: 0.78 µM), Lidocaine HCl (Ki: 1.78 µM), and Propranolol (Ki: 1.86 µM). Molecular docking was also applied to confirm the activity of some cardiac drugs on PON1.
Predictors of renal impairment and proteinuria after commencement of antiretroviral therapy in a Zimbabwean HIV cohort
Authors: Drak Douglas , Heron Jack E. , Shamu Tinei , Chimbetete Cleophas , Dahwa Rumbi , Gracey David M. 
Published: April 2022

AbstractBackgroundRenal disease prevalence varies widely amongst reported cohorts of people living with HIV (PLWHIV) in sub‐Saharan Africa. Renal function testing is not routine in those commencing antiretroviral therapy (ART) in the region, however. Further data on renal disease prevalence and the change associated with ART use are therefore needed.AimTo explore changes in renal function and associated predictors after 1 year of ART in an adult cohort of PLWHIV from Zimbabwe.MethodsA retrospective analysis of patients who attended the Newlands Clinic between January 2007 and September 2019. Eligible patients were aged ≥18 years and had measures of serum creatinine at baseline and after 1 year of ART. Predictors of renal function change were assessed by multiple linear regression.Results1729 patients were eligible for inclusion. Median age was 36 years (IQR 30–43) and 62.8% were female. After 1 year of ART, the proportion of patients with an estimated glomerular filtration rate (eGFR) <60 ml/min/1.732 did not significantly change (2.0% vs. 1.2%; p = 0.094), but there was a decrease in the proportion of patients with proteinuria (11.0% vs. 5.6%; p < 0.001). Hypertension (B = −6.43; 95% CI −8.97 to −3.89; p < 0.001) and baseline proteinuria (B = −7.33; 95% CI −10.25 to −4.42; p < 0.001) were negative predictors of change in eGFR from baseline, whereas diabetes status was not associated (p = 0.476).ConclusionProteinuria was common, but its prevalence halved after 1 year of ART. Screening for hypertension could be a simple way to identify patients at risk of renal function decline.
A model for early failure prediction of blood pressure measurement devices in a stepped validation approach
Authors: Vischer Annina S. , Dutilh Gilles , Socrates Thenral , Burkard Thilo 
Published: April 2022

AbstractBlood pressure monitoring (BPM) devices have to be validated according to strict international validation protocols. Each protocol requests a specific number of participants to be included. All protocols use vast amounts of resources, as three people have to be present for every measurement, making trials costly, especially when the manufacturer has no intention to execute a validation study, reflected in the low share of validated in the commercially available BPM devices. The aim of our study was to develop criteria, which could detect low accuracy devices that could not pass a validation protocol early in the course of the validation process. The 2010 European Society of Hypertension International Protocol (ESH‐IP) and the Universal Standard for Validation of BPM devices (AAMI/ESH/ISO) were scrutinized for criteria which can be used for preclusion of passing. Based on this, we developed a fail model. We found that a BPM device cannot pass the ESH‐IP protocol, if there are ≥27, 13, or 4 single measurements differing more than 5, 10, or 15 mmHg, respectively, from the reference. For the AAMI/ESH/ISO protocol, we developed a model, which calculates best‐case standard deviations (SDs) to detect SDs which would prevent the passing of the protocol before its completion, making a stepwise validation process possible. In conclusion, we found that our model is able to predict failure of low‐accuracy BPM devices early during a validation protocol if used in a stepwise‐approach. This can be useful to keep costs of validation studies low and to enable investigator‐initiated trials.
Analysis of necroptosis and its association with pyroptosis in organ damage in experimental pulmonary arterial hypertension
Authors: Jarabicová Izabela , Horváth Csaba , Veľasová Eva , Bies Piváčková Lenka , Vetešková Jana , Klimas Ján , Křenek Peter , Adameová Adriana 
Published: April 2022

AbstractIn this study, a role of cell loss due to necroptosis and its linkage with pyroptosis in organ damage under the conditions of pulmonary arterial hypertension (PAH) was examined. Monocrotaline (MCT) was used to induce PAH in Wistar rats, and depending on the severity of the disease progression, they were further divided into two subgroups: MCT group—sacrificed 4 weeks after MCT administration and ptMCT group—prematurely sacrificed due to rapid deterioration in vital functions (on Day 24,11 ± 0,7). The elevation of respiratory rate and right ventricular (RV) hypertrophy were more evident in ptMCT group, while the heart rate and cardiac haemodynamic stress markers were comparably higher in both diseased groups. Detailed immunoblotting analysis revealed that the upregulation of pThr231/Ser232‐RIP3 proceeded into necroptosis execution in the RVs, unlike in the lungs of both PAH stages. The elevated pulmonary pThr231/Ser232‐RIP3 levels in both PAH subgroups were associated rather with GSDMD‐mediated pyroptosis. On the contrary, other inflammasome forms, such as AIM2 and NLRC4, were higher in the RV, unlike in the lungs, of diseased groups. The PAH‐induced increase in the plasma RIP3 levels was more pronounced in ptMCT group, and positively correlated with RV hypertrophy, but not with haemodynamic stress. Taken together, we indicated for the first time that pThr231/Ser232‐RIP3 upregulation resulting in two different necrosis‐like cell death modes might underlie the pathomechanisms of PAH and that the plasma RIP3 might serve as an additional diagnostic and prognostic marker of cardiac injury under these conditions.
Diagnosis, management, and outcome of urethral obstruction secondary to the capsule associated with the artificial urethral sphincter device
Authors: Kopecny Lucy , Palm Carrie A. , Culp William T. N. 
Published: April 2022

AbstractBackgroundUrethral obstruction secondary to artificial urethral sphincter (AUS) implantation is a recognized complication in dogs. However, urethral obstruction secondary to AUS‐associated capsule formation has been described rarely.HypothesisDescribe clinical and diagnostic findings, management, and outcome in 6 dogs with urethral obstruction secondary to AUS‐associated capsule formation.AnimalsSix client‐owned dogs.MethodsRetrospective study. Medical records between January 1, 2010, and June 30, 2021, were reviewed to identify dogs with urethral obstruction associated with the AUS device.ResultsThe AUS device was implanted a median of 884 days (range, 20‐2457 days) before presentation for urethral obstruction. Median age at time of urethral obstruction was 4.7 years (range, 3.1‐8.7 years). Clinical signs at the time of urethral obstruction were stranguria (n = 4), pollakiuria (3), weak urine stream (2), and worsened urinary incontinence (1). In all dogs, the urethra was noted to be stenotic during urethroscopy and positive contrast cystourethrography. All dogs underwent surgery, and a fibrous capsule associated with the AUS was found to be causing urethral stenosis. Resolution of urethral obstruction occurred in all dogs after transection or removal of the capsule. Positive bacterial cultures were obtained from the capsule, AUS, or both in all dogs. Recurrence of urethral obstruction had not occurred in any dog at the time of follow‐up.Conclusions and Clinical ImportanceUrethral obstruction secondary to capsule formation is an uncommon but clinically important complication associated with use of the AUS. Continued investigation is needed to evaluate this complication more thoroughly, and its possible association with infection.
The effect of manganese and iron on mediating resuscitation of lactic acid-injured Escherichia coli
Authors: Zhang H.C. , Zhang R. , Shi H. 
Published: April 2022

Abstract
Lactic acid can induce sublethal injury of E. coli through oxidative stress. In this study, we investigated changes in SOD activity, CAT activity, GSH production and ROS production during sublethal injury and resuscitation of E. coli. Then, the effect of manganese and iron during resuscitation were studied. Both cations (≥1 mmol l−1) significantly promoted the resuscitation of sublethally injured E. coli induced by lactic acid and shortened the repair time (P &lt; 0·05). Conversely, addition of N,N,N′,N′-tetrakis (2-pyridylmethyl) which is a metal chelator extended the repair time. Compared with minA, manganese and iron significantly improved SOD activity at 40, 80 and 120 min and decreased ROS production at 40 and 80 min, thereby recovering injured E. coli quickly (P &lt; 0·05). The deletion of sodA encoding Mn-SOD, sodB encoding Fe-SOD or gshA/gshB encoding GSH significantly strengthened sublethal injury and extended the repair time (P &lt; 0·05). It meant these genes-related oxidative stress played important roles in the acid resistance of E. coli and recovery of sublethal injury. Therefore, manganese and iron can promote the recovery of lactic-injured E. coli by the way of increasing SOD activity, scavenging ROS, and relieving oxidative stress.
Peritoneal dialysis first policy in Hong Kong for 35 years: Global impact
Authors: Li Philip Kam‐Tao , Lu Wanhong , Mak Siu‐Ka , Boudville Neil , Yu Xueqing , Wu Ming Ju , Cheng Yuk‐Lun , Chan Christopher T. , Goh Bak Leong , Tian Na , Chow Kai Ming , Lui Sing Leung , Lo Wai Kei 
Published: April 2022

AbstractPeritoneal dialysis (PD) first policy has been established in Hong Kong since 1985. After 35 years of practice, the PD first policy in Hong Kong has influenced many countries around the world including governments, health ministries, nephrologists and renal nurses on the overall health policy structure and clinical practice in treating kidney failure patients using PD as an important dialysis modality. In 2021, the International Association of Chinese Nephrologists and the Hong Kong Society of Nephrology jointly held a symposium celebrating the 35 years of PD first policy in Hong Kong. In that symposium, experts and opinion leaders from around the world have shared their perspectives on how the PD first policy has grown and how it has affected PD and home dialysis practice globally. The advantages of PD during COVID‐19 pandemic were highlighted and the use of telemedicine as an important adjunct was discussed in treating kidney failure patients to improve the overall quality of care. Barriers to PD and the need for sustainability of PD first policy were also emphasized. Overall, the knowledge awareness of PD as a home dialysis for patients, families, care providers and learners is a prerequisite for the success of PD first. A critical mass of PD regional hubs is needed for training and mentorship. Importantly, the alignment of policy and clinical goals are enablers of PD first program.
Pictograms are more effective than verbal descriptors in Spanish for bloating and distension
Authors: Rábago Ruth , Bonilla Alejandro , Escamilla‐Diego Ernesto , Higuera de la Tijera María Fátima , Schmulson Max 
Published: April 2022

AbstractBackgroundThere is no translation for bloating in Spanish, and distension is very technical.AimsTo evaluate pictograms for assessing bloating/distension in patients with general gastroenterology (Study 1, n = 88) and in those with irritable bowel syndrome [IBS] (Study 2: n = 144), and to correlate them with verbal descriptors (VDs) and physician's diagnosis (PDx).MethodsPatients answered the Rome III Questionnaire with VDs and pictograms, and were consulted by two gastroenterology fellows (PDx). Correlations were conducted with Cohen's kappa, and ROC curves were used to contrast pictograms and VDs with PDx.Results“Inflammation” was the most frequent VDs, while distension was commonly interpreted as a sensation (“inflammation”) and/or increased abdominal girth. In patients not reporting bloating/distension with VDs, pictograms detected these symptoms in (Study 1 and Study 2) 82.2 and 89.6% of patients. In addition, pictograms showed a positive agreement with PDx, kappa: 0.63 (p < 0.0001) and 0.8 (p < 0.0001); and a negative agreement with VD, kappa: −0.45 (p = 0.05) and −0.1 (p = 0.2), respectively, in studies 1 and 2. Pictograms were more sensitive and specific than VDs (Study 1: ROC = 0.90 (95% CI: 0.80–0.96), p < 0.0001 versus 0.74 (0.62–0.88), p < 0.0001; Study 2: 0.99 (0.98–1.00), p = 0.004 versus 0.32 (0.10‐0.54), p = 0.294).ConclusionsPictograms are more effective than Spanish VDs for bloating/distension in patients consulting for gastroenterology problems and those with IBS, supporting their usefulness in the clinic and research studies.