bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observation of aerosol induced ‘lower tropospheric cooling’ over Indian core monsoon region
Authors: Jangid Manish , Mishra Amit Kumar , Koren Ilan , Sarangi Chandan , Kumar Krishan , Singh Sachchidanand , Tripathi Sachchidanand 
Published: November 2021

Abstract
Aerosols play a significant role in regional scale pollution that alters the cloud formation process, radiation budget, and climate. Here, using long-term (2003–2019) observations from multi-satellite and ground-based remote sensors, we show robust aerosol-induced instantaneous daytime lower tropospheric cooling during the pre-monsoon season over the Indian core monsoon region (ICMR). Quantitatively, an average cooling of −0.82 °C ± 0.11 °C to −1.84 °C ± 0.25 °C is observed in the lower troposphere. The observed cooling is associated with both aerosol-radiation and aerosol-cloud-radiation interaction processes. The elevated dust and polluted-dust layers cause extinction of the incoming solar radiation, thereby decreasing the lower tropospheric temperature. The aerosol-cloud interactions also contribute to enhancement of cloud fraction which further contributes to the lower tropospheric cooling. The observed cooling results in a stable lower tropospheric structure during polluted conditions, which can also feedback to cloud systems. Our findings suggest that aerosol induced lower tropospheric cooling can strongly affect the cloud distribution and circulation dynamics over the ICMR, a region of immense hydroclimatic importance.
Lattice star and acyclic branched polymer vertex exponents in 3d
Authors: Campbell S , Janse van Rensburg EJ 
Published: November 2021

Abstract
Numerical values of lattice star entropic exponents γ

f
, and star vertex exponents σ

f
, are estimated using parallel implementations of the PERM and Wang–Landau algorithms. Our results show that the numerical estimates of the vertex exponents deviate from predictions of the ϵ-expansion and confirms and improves on estimates in the literature. We also estimate the entropic exponents

γ

G

of a few acyclic branched lattice networks with comb and brush connectivities. In particular, we confirm within numerical accuracy the Duplantier scaling relation

γ

G

−
1
=

∑

f
⩾
1

m

f

σ

f

for a comb and two brushes (where m

f
is the number of nodes of degree f in the network) using our independent estimates of σ

f
.
Interfacial structure and mechanical properties of the Ta/Re layered composites prepared by chemical vapor deposition
Authors: Yuan Zhentao , Chen Jingchang , Wei Yan , Hu Changyi , Luo Yuan , Chen Li , Cai Hongzhong , Wang Xiao 
Published: November 2021

Abstract
A novel Ta/Re layered composites with high temperature resistance, low cost, light weight, and excellent mechanical properties has been prepared by chemical vapor deposition, for improving the comprehensive service performance of the aerospace engine nozzle materials. The interface structure, element distribution, and mechanical properties of the Ta/Re layered composites have been studied with scanning electron microscopy, energy dispersive spectroscopy, x-ray diffraction, and tensile testing machine. The results show that the structure of the Ta/Re layered composites is flat and smooth, uniform, and dense. Further, the interface joint is a serrated meshing structure, which tremendously improves the interface bonding properties. The high temperature (1600 °C) tensile strength of the heat-treated Ta/Vol. 30% Re layered composites is 125 MPa, which is 2.8 times and 56.3% higher than the commonly used nozzle materials C103 and Nb521, respectively, whereas the raw material cost is only about 46% of that of pure rhenium. The heat treatment process enhances the mutual diffusion behavior of the atoms in the interface diffusion layer, and increases the thickness of the diffusion layer, besides changing the mechanical properties of the material. When the heat treatment process is at 1800 °C × 1 h, the highest tensile strength at room temperature is 739.61 MPa, which is 42.76% higher than that in a deposited state. This work can provide a reference for the further research of the Ta/Re layered composites.
Detection of transcription factors binding to methylated DNA by deep recurrent neural network
Authors: Li Hongfei , Gong Yue , Liu Yifeng , Lin Hao , Wang Guohua 
Published: November 2021

Abstract
Transcription factors (TFs) are proteins specifically involved in gene expression regulation. It is generally accepted in epigenetics that methylated nucleotides could prevent the TFs from binding to DNA fragments. However, recent studies have confirmed that some TFs have capability to interact with methylated DNA fragments to further regulate gene expression. Although biochemical experiments could recognize TFs binding to methylated DNA sequences, these wet experimental methods are time-consuming and expensive. Machine learning methods provide a good choice for quickly identifying these TFs without experimental materials. Thus, this study aims to design a robust predictor to detect methylated DNA-bound TFs. We firstly proposed using tripeptide word vector feature to formulate protein samples. Subsequently, based on recurrent neural network with long short-term memory, a two-step computational model was designed. The first step predictor was utilized to discriminate transcription factors from non-transcription factors. Once proteins were predicted as TFs, the second step predictor was employed to judge whether the TFs can bind to methylated DNA. Through the independent dataset test, the accuracies of the first step and the second step are 86.63% and 73.59%, respectively. In addition, the statistical analysis of the distribution of tripeptides in training samples showed that the position and number of some tripeptides in the sequence could affect the binding of TFs to methylated DNA. Finally, on the basis of our model, a free web server was established based on the proposed model, which can be available at https://bioinfor.nefu.edu.cn/TFPM/.
Respiratory Syncytial Virus, Human Metapneumovirus, and Parainfluenza Virus Infections in Lung Transplant Recipients: A Systematic Review of Outcomes and Treatment Strategies
Authors: de Zwart Auke , Riezebos-Brilman Annelies , Lunter Gerton , Vonk Judith , Glanville Allan R , Gottlieb Jens , Permpalung Nitipong , Kerstjens Huib , Alffenaar Jan-Willem , Verschuuren Erik 
Published: November 2021

Abstract

Background
Respiratory syncytial virus (RSV), parainfluenza virus (PIV), and human metapneumovirus (hMPV) are increasingly associated with chronic lung allograft dysfunction (CLAD) in lung transplant recipients (LTR). This systematic review primarily aimed to assess outcomes of RSV/PIV/hMPV infections in LTR and secondarily to assess evidence regarding the efficacy of ribavirin.

Methods
Relevant databases were queried and study outcomes extracted using a standardized method and summarized.

Results
Nineteen retrospective and 12 prospective studies were included (total 1060 cases). Pooled 30-day mortality was low (0–3%), but CLAD progression 180–360 days postinfection was substantial (pooled incidences 19–24%) and probably associated with severe infection. Ribavirin trended toward effectiveness for CLAD prevention in exploratory meta-analysis (odds ratio [OR] 0.61, [0.27–1.18]), although results were highly variable between studies.

Conclusions
RSV/PIV/hMPV infection was followed by a high CLAD incidence. Treatment options, including ribavirin, are limited. There is an urgent need for high-quality studies to provide better treatment options for these infections.
An inverse DEA model for intermediate and output target setting in serially linked general two-stage processes
Authors: Kazemi Ahmad , Galagedera Don U A 
Published: November 2021

Abstract
In this paper, we formulate an inverse data envelopment analysis (DEA) model for a serially linked two-stage production process operating under constant returns to scale technology. The inverse DEA model determines a set of intermediate and output targets for an input augmented decision-making unit (DMU) to maintain its relative efficiency at a pre-specified level. We solve the inverse DEA model using the constraint method used in multi-objective optimization. The input augmented DMU with intermediate and output targets obtained in the inverse DEA model is a hypothetical DMU. Under our modelling framework, when such a hypothetical DMU established on an inefficient DMU is included in the observed DMU set, the frontier established with observed DMU set remains intact. This is important in practice as the intermediate and output targets of the hypothetical DMU would be feasible. When overall efficiency of the hypothetical DMU is decomposed, individual stages have the same efficiency level as that of the hypothetical DMU. This is important to DMU managers as sub-processes also maintain the desired overall efficiency level. We apply our inverse DEA model to a sample of Australian superannuation funds. We demonstrate that each unique Pareto optimal solution of the inverse DEA model obtained through the constraint method provides a specific set of intermediate and output targets and they may offer trade-off between intermediates and outputs. When fund managers anticipate expansion or growth in their funds, choice of targets allows comparison of different trade-off scenarios and makes informed decisions.
Performance of Japanese patients in registrational studies
Authors: Goto Yasushi , Arakawa Sayaka , Shirasawa Masayuki , Higashiyama Ryoko , Baba Keisuke , Masuda Ken , Shinno Yuki , Matsumoto Yuji , Okuma Yusuke , Yoshida Tatsuya , Horinouchi Hidehito , Yamamoto Noboru , Ohe Yuichiro 
Published: November 2021

Abstract

Introduction
The accelerated development of lung cancer treatments has resulted in a single global study that is sufficient for a new agent and indication to be approved. Not all new treatments predominate globally, and differences in standards of care may influence the efficacy of treatments in the real world.

Methods
The results from Japanese domestic trials and global trials that included a subset population of Japanese patients were evaluated for 18 genomic targeted agents and immune therapies approved after 2000. The results were collected from drug applications that were reviewed for treatment approval in Japan.

Results
Japan is one of the first countries to approve and fully reimburse new agents around the world. Alectinib and nivolumab, which were first developed by Japanese pharmaceutical companies, were evaluated in an independent domestic trial, which resulted in their early approval. For most other indications, 1.1–15.8% of the patients who participated in pivotal registration studies were Japanese, and their treatment results were comparable to those of the overall population. Overall survival was less likely to be improved by four agents for which the post-protocol therapy might have been different in Japan than in other countries.

Conclusions
Overall, a positive result in a global trial was emulated in Japanese patients and led to the approval of a new standard treatment in Japan. Early approvals were attained by either participating in the global registrational study or conducting a domestic phase II study. The higher efficacy of new agents may be an issue in the future, as Japanese patients had early access to the new agent and may receive better treatment after the trial.
Clinical relevance of addition of conventional treatment to concurrent chemoradiotherapy in patients with FIGO stage III–IV cervical cancer: a retrospective analysis of a Japanese cohort
Authors: Kurosu Hiroyuki , Todo Yukiharu , Yamada Ryutaro , Minowa Kaoru , Tsuruta Tomohiko , Minobe Shinichiro , Nishiyama Noriaki , Kato Hidenori 
Published: November 2021

Abstract

Background
Concurrent chemoradiotherapy has limited therapeutic efficacy for stage III–IV cervical cancer. We aimed to identify a subgroup of patients with stage III–IV cervical cancer who benefit from concurrent chemoradiotherapy with additional treatment.

Methods
We retrospectively reviewed 120 patients with stage III–IV cervical cancer who were treated with concurrent chemoradiotherapy from 2002 to 2018. We compared overall survival between patients treated with concurrent chemoradiotherapy alone and those who received concurrent chemoradiotherapy with additional conventional treatments (systemic chemotherapy before and/or after concurrent chemoradiotherapy and/or extended-field radiation). Prognostic factors were statistically analysed.

Results
Overall, 44 (36.7%) and 21 (17.5%) patients were radiologically diagnosed with pelvic and para-aortic lymph node enlargement, respectively. The median tumour diameter was 5.7 cm. A total of 69 (57.5%) patients received no additional treatment, and 51 (42.5%) received additional treatment. Cox regression analysis identified the following prognostic factors: histological non-squamous cell carcinoma (hazard ratio, 3.9; 95% confidence interval, 1.8–8.2), tumour diameter of ≥6 cm (hazard ratio, 2.1; 95% confidence interval, 1.2–3.7), radiological pelvic lymph node enlargement (hazard ratio, 2.1; 95% confidence interval, 1.1–4.0) and radiological para-aortic lymph node enlargement (hazard ratio, 2.1; 95% confidence interval, 1.1–4.1). Even in the lowest risk group (no risk factors), the 5-year overall survival rate was lower in the additional treatment group than in the concurrent chemoradiotherapy alone group (78.7% vs. 80.9%, respectively; log-rank test, P = 0.79).

Conclusions
Addition of conventional treatments to concurrent chemoradiotherapy might not improve survival in patients with advanced cervical cancer. Novel treatment strategies including immune checkpoint inhibitors should be considered for such patients.
Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons
Authors: Heringer Pedro , Kuhn Gustavo C S 
Published: November 2021

Abstract
Helitrons are the only group of rolling-circle transposons that encode a transposase with a helicase domain (Hel), which belongs to the Pif1 family. Because Pif1 helicases are important components of eukaryotic genomes, it has been suggested that Hel domains probably originated after a host eukaryotic Pif1 gene was captured by a Helitron ancestor. However, the few analyses exploring the evolution of Helitron transposases (RepHel) have focused on its Rep domain, which is also present in other mobile genetic elements. Here, we used phylogenetic and nonmetric multidimensional scaling analyses to investigate the relationship between Hel domains and Pif1-like helicases from a variety of organisms. Our results reveal that Hel domains are only distantly related to genomic helicases from eukaryotes and prokaryotes, and thus are unlikely to have originated from a captured Pif1 gene. Based on this evidence, and on recent studies indicating that Rep domains are more closely related to rolling-circle plasmids and phages, we suggest that Helitrons are descendants of a RepHel-encoding prokaryotic plasmid element that invaded eukaryotic genomes before the radiation of its major groups. We discuss how a Pif1-like helicase domain might have favored the transposition of Helitrons in eukaryotes beyond simply unwinding DNA intermediates. Finally, we demonstrate that some examples in the literature describing genomic helicases from eukaryotes actually consist of Hel domains from Helitrons, a finding that underscores how transposons can hamper the analysis of eukaryotic genes. This investigation also revealed that two groups of land plants appear to have lost genomic Pif1 helicases independently.
Population Histories and Genomic Diversity of South American Natives
Authors: Castro e Silva Marcos Araújo , Ferraz Tiago , Couto-Silva Cainã M , Lemes Renan B , Nunes Kelly , Comas David , Hünemeier Tábita 
Published: November 2021

Abstract
South America is home to one of the most culturally diverse present-day native populations. However, the dispersion pattern, genetic substructure, and demographic complexity within South America are still poorly understood. Based on genome-wide data of 58 native populations, we provide a comprehensive scenario of South American indigenous groups considering the genomic, environmental, and linguistic data. Clear patterns of genetic structure were inferred among the South American natives, presenting at least four primary genetic clusters in the Amazonian and savanna regions and three clusters in the Andes and Pacific coast. We detected a cline of genetic variation along a west-east axis, contradicting a hard Andes-Amazon divide. This longitudinal genetic variation seemed to have been shaped by both serial population bottlenecks and isolation by distance. Results indicated that present-day South American substructures recapitulate ancient macroregional ancestries and western Amazonia groups show genetic evidence of cultural exchanges that led to language replacement in precontact times. Finally, demographic inferences pointed to a higher resilience of the western South American groups regarding population collapses caused by the European invasion and indicated precontact population reductions and demic expansions in South America.
Rice as a vehicle for micronutrient fortification: a systematic review of micronutrient retention, organoleptic properties, and consumer acceptability
Authors: Pyo Euisun , Tsang Becky L , Parker Megan E 
Published: November 2021

AbstractContextPrevious reviews have focused on evaluating the efficacy and effectiveness of rice fortification, despite the need to also understand the outcomes of micronutrient retention, organoleptic properties, and acceptability to inform nutrition programs.ObjectiveThis systematic review aims to consolidate existing evidence on micronutrient retention, organoleptic properties, and acceptability of fortified rice.Data SourcesEligible articles were identified from 22 electronic databases and personal referrals and reviews.Study SelectionStudies on rice fortified via extrusion or coating technologies were included in the review if they reported outcomes in at least 1 of 3 domains: micronutrient retention, organoleptic or physicochemical properties, and acceptability (evaluated by sensory tests and consumer surveys). Any years of publication and study populations were considered for inclusion. A total of 15 391 articles were screened, yielding 49 for inclusion.Data ExtractionStudy results were summarized descriptively through discussions by intervention conditions, study population, measurement methods, and key findings. The included studies were independently reviewed by 2 of the 3 authors, and all 3 authors reached consensus on the quality and major findings from the included articles.ResultsExtrusion and coating fortification technologies were found to be comparable across studies that assessed retention, organoleptic properties, and acceptability. Cooking fortified rice in excess water increased micronutrient loss for both technologies. Fortified kernels containing ferric pyrophosphate, zinc oxide, or zinc sulfate showed the most positive results for all outcomes reviewed, while retention rates of vitamin A in multiple-micronutrient-fortified rice were variable.ConclusionsThe current practice of fortifying rice with ferric pyrophosphate provides high micronutrient stability and results in rice with organoleptic properties and consumer acceptance levels comparable to those of unfortified milled rice, although it presents challenges regarding the effect of vitamin A–fortified rice on vitamin A status.
The Incidence of Iliac Screw-Related Complications After Long Fusion Surgery in Patients with Adult Spinal Deformity
Authors: Banno Tomohiro , Hasegawa Tomohiko , Yamato Yu , Yoshida Go , Arima Hideyuki , Oe Shin , Mihara Yuki , Ide Koichiro , Watanabe Yuh , Kurosu Kenta , Nakai Keiichi , Matsuyama Yukihiro 
Published: November 2021

Study Design.
Retrospective study.

Objective.
To investigate the long-term clinical outcome and incidence of iliac screw-related complications in patients with adult spinal deformity (ASD).

Summary of Background Data.
Rigid lumbosacral fixation is crucial to achieve optimal global alignment and successful long-term clinical outcomes.

Methods.
The data of eligible patients with ASD who underwent spinopelvic fixation using bilateral iliac screws with at least 5-year follow-up periods were retrospectively analyzed. Iliac screw loosening and rod breakage between the S1 and iliac (S1/IL) screws were defined as distal instability (DI). Demographic data, health-related quality of life scores, and spinopelvic parameters in the DI group were compared with those in the non-DI group. Sub-group analyses were performed between the cases with and without alignment change after rod fracture at S1/IL.

Results.
Of the 159 patients, the data of 110 patients (15 men, 95 women; mean age, 67.8 yr) were analyzed. The follow-up rate was 69%. Forty-five (41%) patients showed DI (29 cases [26%] in screw loosening, 16 cases [15%] in rod breakage). Eight patients (7.3%) required revision surgery because of iliac screw-related complications. No significant differences were observed in the Oswestry Disability Index and Scoliosis Research Society questionnaire (revised) scores between the DI and non-DI groups. The patients with iliac screw loosening showed significantly greater values of preoperative pelvic incidence, pelvic tilt (PT), and postoperative PT, and T1-pelvic angle. In patients with rod breakage at S1/IL, five patients (31%) who had associated mechanical complications showed an alignment change between pre and post rod breakage. They showed significantly higher and lower rates of high-grade osteotomies and L5/S interbody fusion, respectively.

Conclusion.
The incidence rate of iliac screw-related complications was relatively high. However, they had a little effect on sagittal alignment deterioration and there were few cases that required revision surgery.

Level of Evidence: 4