bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring hidden phenotype: quantifying the shape of barley seeds using the Euler characteristic transform
Authors: Amézquita Erik J , Quigley Michelle Y , Ophelders Tim , Landis Jacob B , Koenig Daniel , Munch Elizabeth , Chitwood Daniel H 
Published: December 2021

Abstract
Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare and analyse this information embedded in a robust and concise way, we turn to topological data analysis (TDA), specifically the Euler characteristic transform. TDA measures shape comprehensively using mathematical representations based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to quantify the morphology of 3121 barley seeds scanned with X-ray computed tomography (CT) technology at 127 μm resolution. The Euler characteristic transform measures shape by analysing topological features of an object at thresholds across a number of directional axes. A Kruskal–Wallis analysis of the information encoded by the topological signature reveals that the Euler characteristic transform picks up successfully the shape of the crease and bottom of the seeds. Moreover, while traditional shape descriptors can cluster the seeds based on their accession, topological shape descriptors can cluster them further based on their panicle. We then successfully train a support vector machine to classify 28 different accessions of barley based exclusively on the shape of their grains. We observe that combining both traditional and topological descriptors classifies barley seeds better than using just traditional descriptors alone. This improvement suggests that TDA is thus a powerful complement to traditional morphometrics to comprehensively describe a multitude of ‘hidden’ shape nuances which are otherwise not detected.
QbD-Based Development and Validation of Novel Stability-Indicating Method for the Assay and Dissolution of Garenoxacin in Garenoxacin Tablets
Authors: Azhakesan Ajitha , Kuppusamy Sujatha 
Published: December 2021

Abstract

Background
Garenoxacin mesylate is a novel des-fluoro(6) quinolone, approved and marketed for human use in Japan under the name Geninax.

Objective
In this current work, a simple and stability-indicating method for the assay and dissolution of garenoxacin in garenoxacin tablets 200 mg was performed. New method developed for the particle size measurement of Garenoxacin mesylate Active Pharmaceutical Ingredient using Malvern 2000.

Methods
A quality by design (QbD)-based stability-indicating assay method was developed using 0.1% (v/v) formic acid in water and methanol (70:30). Using a photodiode array detector the peak purity of the garenoxacin peak for all degradation samples was studied. The biopharmaceutical classification system (BCS) solubility of garenoxacin mesylate active pharmaceutical ingredient (API) was studied by a modified shake flask method. A dissolution test method was developed using 0.1 N hydrochloric acid as the medium, United State Pharmacopoeia apparatus-II (paddle), revolution per minute (rpm) 50, temperature 37 ± 0.5°C and time 30 min. Liquid paraffin was used as the dispersant in the particle size measurement of garenoxacin mesylate API using the Malvern Mastersizer—wet method.

Results
The QbD-based RP-HPLC method was stability-indicating, simple, precise, and accurate. The assay method was linear over 12.5 to 75 µg/mL at the detection wavelength of 280 nm. A UV-based method was developed and validated for the dissolution of garenoxacin 200 mg tablets and the method was found to be linear over 2.9 to 34.2 µg/mL at 280 nm. Based on data, the dissolution tolerance for garenoxacin 200 mg tablets was proposed as Q not less than 80% at time 30 min (% drug released with respect to label claim (Q). The effect of garenoxacin mesylate API particle size in the tablet dosage form was studied using particles of 92 µm and 220 µm [90% of the total particles are smaller than this size (D90)] and it was found that there was no impact on the in vitro dissolution profile.

Conclusion
The reported stability-indicating assay and dissolution test methods can be used in regular QC testing of garenoxacin 200 mg tablets. The Malvern particle size wet dispersion measurement method developed and validated for garenoxacin mesylate API is simple and robust.

Highlights
A QbD based RP-HPLC method (using Design Expert Software version 11) was developed and studied peak purity of Garenoxacin peak using Photo Diode Array detector (for all degradation samples, control sample and standard solution) and the same method is validated following USP and ICH guidelines. LC–MS compatible volatile buffer solution is used in the preparation of the mobile phase for the novel stability-indicating RP-HPLC assay method.
Efficient approximation of reliabilities for single-step genomic best linear unbiased predictor models with the Algorithm for Proven and Young
Authors: Bermann Matias , Lourenco Daniela , Misztal Ignacy 
Published: December 2021

AbstractThe objectives of this study were to develop an efficient algorithm for calculating prediction error variances (PEVs) for genomic best linear unbiased prediction (GBLUP) models using the Algorithm for Proven and Young (APY), extend it to single-step GBLUP (ssGBLUP), and apply this algorithm for approximating the theoretical reliabilities for single- and multiple-trait models in ssGBLUP. The PEV with APY was calculated by block sparse inversion, efficiently exploiting the sparse structure of the inverse of the genomic relationship matrix with APY. Single-step GBLUP reliabilities were approximated by combining reliabilities with and without genomic information in terms of effective record contributions. Multi-trait reliabilities relied on single-trait results adjusted using the genetic and residual covariance matrices among traits. Tests involved two datasets provided by the American Angus Association. A small dataset (Data1) was used for comparing the approximated reliabilities with the reliabilities obtained by the inversion of the left-hand side of the mixed model equations. A large dataset (Data2) was used for evaluating the computational performance of the algorithm. Analyses with both datasets used single-trait and three-trait models. The number of animals in the pedigree ranged from 167,951 in Data1 to 10,213,401 in Data2, with 50,000 and 20,000 genotyped animals for single-trait and multiple-trait analysis, respectively, in Data1 and 335,325 in Data2. Correlations between estimated and exact reliabilities obtained by inversion ranged from 0.97 to 0.99, whereas the intercept and slope of the regression of the exact on the approximated reliabilities ranged from 0.00 to 0.04 and from 0.93 to 1.05, respectively. For the three-trait model with the largest dataset (Data2), the elapsed time for the reliability estimation was 11 min. The computational complexity of the proposed algorithm increased linearly with the number of genotyped animals and with the number of traits in the model. This algorithm can efficiently approximate the theoretical reliability of genomic estimated breeding values in ssGBLUP with APY for large numbers of genotyped animals at a low cost.
Japanese Beetle (Coleoptera: Scarabaeidae) Invasion of North America: History, Ecology, and Management
Authors: Althoff Emily R , Rice Kevin B 
Published: December 2021

AbstractThe Japanese beetle, Popillia japonica Newman, was accidentally introduced to the United States from Asia in the early 1900s. First detected in a New Jersey nursery, it is currently established in 28 states in the United States and has been detected in 13 additional states, 3 Canadian provinces, and at least 3 European nations. Adult beetles feed on over 300 host plant species, including many agricultural commodities such as fruits, field crops, and ornamentals, often causing severe economic damage. We discuss invasion history, ecology, biology, and management options for this invasive pest species in North America.
Discovery of a luminous starburst galaxy with hundreds of thousands of Wolf–Rayet stars
Authors: Yuan Anqi , Yang Chenwei , Zhong Guohu , Xiao Lin , Pan Xiang , Zhou Hongyan 
Published: December 2021

ABSTRACT
This paper reports the detection of a strong Wolf–Rayet (W-R) emission bump feature at 4400–4700 Å in the optical spectrum of a distant galaxy SDSS J150009.81+452844.4 at a redshift of 0.453. The estimated number of W-R stars is 1.5 × 105 without applying any internal extinction correction, and at least 4.5 × 105 after correcting for dust extinction. Such a number, though with uncertainties inherent from the extinction correction and others, appears to outnumber those in previous W-R galaxies after correcting for intrinsic dust extinction with the numbers available in the literature. These massive stars must have formed in an instantaneous star-forming episode lasting less than about 5 Myr. We estimate a star formation rate of at least ∼80 $\mathrm{M}_{\odot }\, \mathrm{yr^{-1}}$, indicative of a violent starburst. Its mid-infrared spectrum resembles closely those of typical local ultraluminous infrared galaxies (ULIRGs). From optical to ultraviolet, it possesses a luminous blue continuum, indicating that the starburst is not heavily obscured, in contrast to that found in most ULIRGs. There is evidence for strong outflows based on the detection of systematically blue-shifted broad wings in the nebular emission lines (a bulk velocity −190 km s−1), as well as in the blue-shifted Mg ii absorption lines. The emission-line gases show a wide velocity range, from −1200 to ∼−2000 km s−1 in blueshift to 570 km s−1 in redshift. We interpret this as a galactic fountain, of which part of the outflowing gas may be falling back to the galactic plane. Our method could be used to find a sample of similar objects, which would help understand the star formation history and stellar feedback in starburst galaxies.
The incidence of X-ray selected AGN in nearby galaxies
Authors: Birchall Keir L , Watson M G , Aird J , Starling R L C 
Published: December 2021

ABSTRACT
We present the identification and analysis of an unbiased sample of active galactic nuclei (AGN) that lie within the local galaxy population. Using the MPA-JHU catalogue (based on SDSS DR8) and 3XMM DR7 we define a parent sample of 25 949 local galaxies (z ≤ 0.33). After confirming that there was strictly no AGN light contaminating stellar mass and star-formation rate calculations, we identified 917 galaxies with central, excess X-ray emission likely originating from an AGN. We analysed their optical emission lines using the BPT diagnostic and confirmed that such techniques are more effective at reliably identifying sources as AGN in higher mass galaxies: rising from 30 per cent agreement in the lowest mass bin to 93 per cent in the highest. We then calculated the growth rates of the black holes powering these AGN in terms of their specific accretion rates (∝LX/M*). Our sample exhibits a wide range of accretion rates, with the majority accreting at rates $\le 0.5\ \mathrm{ per \, cent}$ of their Eddington luminosity. Finally, we used our sample to calculate the incidence of AGN as a function of stellar mass and redshift. After correcting for the varying sensitivity of 3XMM, we split the galaxy sample by stellar mass and redshift and investigated the AGN fraction as a function of X-ray luminosity and specific black hole accretion rate. From this we found the fraction of galaxies hosting AGN above a fixed specific accretion rate limit of 10−3.5 is constant (at $\approx 1\ \mathrm{ per \, cent}$) over stellar masses of 8 &lt; log M*/M⊙ &lt; 12 and increases (from $\approx 1\ \mathrm{ per \, cent}$ to 10 per cent) with redshift.
Risk factors for low back pain increase in rheumatoid arthritis: Analysis of a 7-year follow-up study
Authors: Yamada Kentaro , Suzuki Akinobu , Takahashi Shinji , Inui Kentaro , Koike Tatsuya , Okano Tadashi , Yabu Akito , Hori Yusuke , Toyoda Hiromitsu , Nakamura Hiroaki 
Published: December 2021

ABSTRACT

Objective
Several studies have demonstrated that low back pain (LBP) is related to disease activity in patients with rheumatoid arthritis (RA). However, there is no longitudinal research. This study aimed to determine the impacts and risk factors for LBP increase in RA in a longitudinal cohort study.

Methods
The study evaluated 113 patients with RA who completed the secondary survey. LBP increase was defined as ≥1 standard deviation of mean change in visual analogue scale (VAS) between the baseline and secondary surveys. The impacts of LBP increase on quality of life (QOL) and psychological status were evaluated. Risk factors were assessed among patient demographic characteristics and radiological changes.

Results
Mean change in VAS for LBP was −0.8 ± 30.4 mm during a mean 7-year follow-up. LBP increase was defined as ≥30-mm increase in VAS for LBP. Patients with LBP increase had significantly lower QOL and worse mental status than patients without it. Poor control of RA was identified as an independent risk factor for LBP increase (odds ratio, 9.82, p = .001).

Conclusion
Patients with poor control of RA were likely to experience LBP increase in the long term. Control of RA disease activity is important for control of LBP, QOL, and mental status.
The management of lupus nephritis as proposed by EULAR/ERA 2019 versus KDIGO 2021
Authors: Anders Hans-Joachim , Loutan Jerome , Bruchfeld Annette , Fernández-Juárez Gema M , Floege Jürgen , Goumenos Dimitrios , Turkmen Kultigin , van Kooten Cees , Frangou Eleni , Stevens Kate I , Kronbichler Andreas , Segelmark Mårten , Tesar Vladimir 
Published: December 2021

ABSTRACTIn 2019 and 2021, the European League for Rheumatism (EULAR) jointly with the European Renal Association (ERA) and the Kidney Disease: Improving Global Outcomes (KDIGO), respectively, released updated guidelines on the management of lupus nephritis (LN). The Immunology Working Group of the ERA reviewed and compared both updates. Recommendations were either consistent or differences were of negligible clinical relevance for: indication for kidney biopsy, kidney biopsy interpretation, treatment targets, hydroxychloroquine dosing, first-line initial immunosuppressive therapy for active class III, IV (±V) LN, pregnancy in LN, LN in paediatric patients and LN patients with kidney failure. Relevant differences in the recommended management relate to the recognition of lupus podocytopathies, uncertainties in steroid dosing, drug preferences in specific populations and maintenance therapy, treatment of pure class V LN, therapy of recurrent LN, evolving alternative drug options and diagnostic work-up of thrombotic microangiopathy. Altogether, both documents provide an excellent guidance to the growing complexity of LN management. This article endeavours to prevent confusion by identifying differences and clarifying discrepancies.
Evaporation of black holes in flat space entangled with an auxiliary universe
Authors: Miyata Akihiro , Ugajin Tomonori 
Published: December 2021

Abstract
We study a thermofield double type entangled state on two disjoint universes A and B, where one of the universes is asymptotically flat containing a black hole. As we increase the entanglement temperature, this black hole receives back-reaction from the stress–energy tensor of the state. This results in lengthening of the wormhole region in the black hole interior, and decreasing of its horizon area, both of which are key features of an evaporating black hole. We then compute the entanglement entropy in universe A through the island formula, and argue that it naturally follows the Page curve of an evaporating black hole in flat space. We also study the effects of local operations in the gravitating universe with the black hole. We find that they accelerate the evaporation of the black hole, thereby disrupting the entanglement between the two universes. Furthermore, we observe that, depending on whether the operation can be regarded as a local operation and classical communication or not, the behavior of the entanglement entropy changes. In particular, when the operation is made neither in the entanglement wedge of the radiation system nor that of the black hole, the transition between the island phase and the no-island phase can happen multiple times.
Fluoroquinolones
Authors: Kidd Tara , Mitchell Stephanie , Dehays Julie , Wibberley Erica 
Published: December 2021

Abstract:
Fluoroquinolones (FQs) are highly effective, well-tolerated, broad-spectrum antibiotics, making them desirable treatment options for infections. However, their adverse reactions as well as recent trends in antibiotic susceptibility must be considered. This article discusses the spectrum of activity and adverse reactions of FQs to guide nurses in caring for patients receiving this class of antibiotics.
Proton Beam Therapy for Locally Advanced Head and Neck Tumors
Authors: Sheikh Saad , Kharouta Michael Z. , Pidikiti Rajesh , Damico Nicholas J. , Choi Serah , Dorth Jennifer A. , Mansur David B. , Machtay Mitchell X. , Yao Min , Bhatt Aashish D. 
Published: December 2021

Objective:
Locally advanced tumors of the head and neck region often lie in close proximity to critical organs at risk (OARs). Providing effective treatment coverage to these malignancies while minimizing radiation dose to surrounding OARs is advantageous. Our aim is to compare dosimetric data of OARs from proton beam therapy (PBT) plans to volumetric modulated arc therapy (VMAT) treatment plans, and to evaluate clinical outcomes in patients treated with PBT.

Methods:
We identified patients with locally advanced head and neck tumors treated with PBT at our institution from 2016 to 2019. Study endpoints included mean and maximum doses for the OAR structures for each treatment plan, overall survival, time to local-regional or distant progression, and presence of acute and late toxicities. Mean and maximum doses to OAR structures were compared between treatment modalities using a paired Wilcoxon signed-rank test. P-values <0.05 were considered significant.

Results:
A total of 42 patients were identified. Clinical target volume coverage was >95% for both PBT and VMAT plans. PBT plans showed a significant reduction to the mean doses to all OARs, and max doses to most OARs (P<0.05). The largest reduction mean dose was seen in the contralateral cochlea and parotid glands at 71% and 75%, respectively. Median follow-up was 27 months. Overall survival at 4 years was 44.75%. Freedom from local-regional progression was 73.28% at 2 years. The majority of patients developed Common Terminology Criteria for Adverse Events (CTCAE) grade I dermatitis, mucositis, or both.

Conclusions:
PBT resulted in meaningful dose reductions to OARs while maintaining comparable target coverage when compared with VMAT plans. Further refinements to proton therapy may have the potential to further minimize dose to critical structures
COVID-19 induced renal injury differs from that in other viral-infections
Authors: Parise Rachel S. , Govindarajulu Manoj , Ramesh Sindhu , Thomas Tony , Moore Timothy , Dhanasekaran Muralikrishnan 
Published: December 2021

Abstract

Background:
Kidney injuries caused by several viral diseases have been reported worldwide among all age groups, races, and genders. Of particular importance is coronavirus disease 2019 (COVID-19), and its prevalence in communities infecting all patient populations with symptoms ranging from asymptomatic to severe, including complications and mortality.

Methods:
Data were acquired from PubMed, Scopus, Google Scholar, Centers for Disease Prevention and Control (CDC), and Lexi-Comp using the following search terms: “COVID-19 and renal pathology,” “COVID-19 induced kidney disease,” “Viral infection induced kidney disease,” and “Viral infection induced renal damage.” Titles and abstracts were manually analyzed as per the exclusion and inclusion criteria of relevant articles; relevance of articles included studies on the pathology of a specific viral infection and the impact of the virus on the adult renal system.

Results:
The mechanisms for renal disease due to COVID-19 include direct renal tubular injury, cytokine storm, inflammation, thrombosis vs. acute tubular necrosis, thrombotic events, and direct renal injury. Although some mechanisms behind renal dysfunction among the studied viral infections are similar, the prevalence rates of kidney injury or damage differ. This might be described by recommended prophylactic and therapeutic approaches that can alter the viral infection characteristics and possibly the impact a particular organ system.

Conclusion:
The patient population at risk was old in age and had a high body mass index. The mechanisms associated with renal dysfunction are similar, including direct renal injury through angiotensin converting enzyme 2 (ACE2) entry, inflammation, and thrombosis. The renal pathology of coronaviruses that differs from that of other prevalent viral infections is the activation of cytokine storm, which causes elevations of a greater number and different kinds of cytokines than other viral infections.
Single-injection regional analgesia techniques for mastectomy surgery
Authors: De Cassai Alessandro , Zarantonello Francesco , Geraldini Federico , Boscolo Annalisa , Pasin Laura , De Pinto Silvia , Leardini Giovanni , Basile Francesca , Disarò Laura , Sella Nicolò , Mariano Edward R. , Pettenuzzo Tommaso , Navalesi Paolo 
Published: December 2021

BACKGROUND
Patients undergoing mastectomy surgery experience severe postoperative pain. Several regional techniques have been developed to reduce pain intensity but it is unclear, which of these techniques is most effective.

OBJECTIVES
To synthesise direct and indirect comparisons for the relative efficacy of different regional and local analgesia techniques in the setting of unilateral mastectomy. Postoperative opioid consumption at 24 h, postoperative pain at extubation, 1, 12 and 24 h, postoperative nausea and vomiting were collected.

DESIGN
Systematic review with network meta-analysis (PROSPERO:CRD42021250651).

DATA SOURCE
PubMed, Scopus, the Cochrane Central Register of Controlled Trials (from inception until 7 July 2021).

ELIGIBILITY CRITERIA
All randomised controlled trials investigating single-injection regional and local analgesia techniques in adult patients undergoing unilateral mastectomy were included in our study without any language or publication date restriction.

RESULTS
Sixty-two included studies randomising 4074 patients and investigating nine techniques entered the analysis. All techniques were associated with less opioid consumption compared with controls The greatest mean difference [95% confidence interval (CI)] was associated with deep serratus anterior plane block: mean difference –16.1 mg (95% CI, –20.7 to –11.6). The greatest reduction in pain score was associated with the interpectoral-pecto-serratus plane block (mean difference —1.3, 95% CI, —1.6 to — 1) at 12 h postoperatively, and with superficial serratus anterior plane block (mean difference —1.4, 95% CI, —2.4 to —0.5) at 24 h. Interpectoral-pectoserratus plane block resulted in the greatest statistically significant reduction in postoperative nausea/vomiting when compared with placebo/no intervention with an OR of 0.23 (95% CI, 0.13 to 0.40).

CONCLUSION
All techniques were associated with superior analgesia and less opioid consumption compared with controls. No single technique was identified as superior to others. In comparison, local anaesthetic infiltration does not offer advantages over multimodal analgesia alone.

TRIAL REGISTRATION
PROSPERO (CRD4202125065).