bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of the squamate naso-palatal complex: detailed 3D analysis of the vomeronasal organ and nasal cavity in the brown anole Anolis sagrei (Squamata: Iguania)
Authors: Kaczmarek Paweł , Janiszewska Katarzyna , Metscher Brian , Rupik Weronika 
Published: September 2020

Abstract
Background
Despite the diverse morphology of the adult squamate naso-palatal complex – consisting of the nasal cavity, vomeronasal organ (VNO), choanal groove, lacrimal duct and superficial palate – little is known about the embryology of these structures. Moreover, there are no comprehensive studies concerning development of the nasal cavity and VNO in relation to the superficial palate. In this investigation, we used X-ray microtomography and histological sections to describe embryonic development of the naso-palatal complex of iguanian lizard, the brown anole (Anolis sagrei). The purpose of the study was to describe the mechanism of formation of adult morphology in this species, which combines the peculiar anole features with typical iguanian conditions. Considering the uncertain phylogenetic position of the Iguania within Squamata, embryological data and future comparative studies may shed new light on the evolution of this large squamate clade.

Results
Development of the naso-palatal complex was divided into three phases: early, middle and late. In the early developmental phase, the vomeronasal pit originates from medial outpocketing of the nasal pit, when the facial prominences are weakly developed. In the middle developmental phase, the following events can be noted: the formation of the frontonasal mass, separation of the vestibulum, appearance of the lacrimal duct, and formation of the choanal groove, which leads to separation of the VNO from the nasal cavity. In late development, the nasal cavity and the VNO attain their adult morphology. The lacrimal duct establishes an extensive connection with the choanal groove, which eventually becomes largely separated from the oral cavity.

Conclusions
Unlike in other tetrapods, the primordium of the lacrimal duct in the brown anole develops largely beyond the nasolacrimal groove. In contrast to previous studies on squamates, the maxillary prominence is found to participate in the initial fusion with the frontonasal mass. Moreover, formation of the choanal groove occurs due to the fusion of the vomerine cushion to the subconchal fold, rather than to the choanal fold. The loss or significant reduction of the lateral nasal concha is secondary. Some features of anole adult morphology, such as the closure of the choanal groove, may constitute adaptations to vomeronasal chemoreception.
gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections
Authors: Louza Felipe A. , Telles Guilherme P. , Gog Simon , Prezza Nicola , Rosone Giovanna 
Published: September 2020

Abstract
Background
The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix array, the Burrows–Wheeler transform, and the document array, are often needed to accompany the suffix array to efficiently solve a wide variety of problems. While several algorithms have been proposed to construct the suffix array for a single string, less emphasis has been put on algorithms to construct suffix arrays for string collections.

Result
In this paper we introduce , an open source software for constructing the suffix array and related data indexing structures for a string collection with N symbols in O(N) time. Our tool is written in and is based on the algorithm gSACA-K (Louza et al. in Theor Comput Sci 678:22–39, 2017), the fastest algorithm to construct suffix arrays for string collections. The tool supports large fasta, fastq and text files with multiple strings as input. Experiments have shown very good performance on different types of strings.

Conclusions
is a fast, portable, and lightweight tool for constructing the suffix array and additional data structures for string collections.
Micronized sacchachitin promotes satellite cell proliferation through TAK1-JNK-AP-1 signaling pathway predominantly by TLR2 activation
Authors: Wu Meng-Huang , Lin Chuang-Yu , Hou Chun-Yin , Sheu Ming-Thau , Chang Hsi 
Published: September 2020

Abstract
Background
Ganoderma sp., such as Ganoderma tsugae (GT), play an important role in traditional Chinese medicine. Ganoderma sp. contains several constituents, including Sacacchin, which has recently drawn attention because it can not only enhance the repair of muscle damage but also strengthen the muscle enforcement. Although Ganoderma sp. have a therapeutic effect for neuromuscular disorders, the underlying mechanism remains unclear. This study investigated the effect and underlying molecular mechanism of micronized sacchachitin (mSC) on satellite cells (SCs), which are known as the muscle stem cells.

Methods
The myogenic cells, included SCs (Pax7+) were isolated from tibialis anterior muscles of a healthy rat and were cultured in growth media with different mSC concentrations. For the evaluation of SC proliferation, these cultivated cells were immunostained with Pax7 and bromodeoxyuridine assessed simultaneously. The molecular signal pathway was further investigated by using Western blotting and signal pathway inhibitors.

Results
Our data revealed that 200 µg/mL mSC had an optimal capability to significantly enhance the SC proliferation. Furthermore, this enhancement of SC proliferation was verified to be involved with activation of TAK1-JNK-AP-1 signaling pathway through TLR2, whose expression on SC surface was confirmed for the first time here.

Conclusion
Micronized sacchachitin extracted from GT was capable of promoting the proliferation of SC under a correct concentration.
Dietary mannose supplementation in phosphomannomutase 2 deficiency (PMM2-CDG)
Authors: Taday Roman , Grüneberg Marianne , DuChesne Ingrid , Reunert Janine , Marquardt Thorsten 
Published: September 2020

Abstract
Background
PMM2-CDG (CDG-Ia) is the most frequent N-glycosylation disorder. While supplying mannose to PMM2-deficient fibroblasts corrects the altered N-glycosylation in vitro, short term therapeutic approaches with mannose supplementation in PMM2-CDG patients have been unsuccessful. Mannose found no further mention in the design of a potential therapy for PMM2-CDG in the past years, as it applies to be ineffective. This retrospective study analyzes the first long term mannose supplementation in 20 PMM2-CDG patients. Mannose was given at a total of 1–2 g mannose/kg b.w./d divided into 5 single doses over a mean time of 57,75 ± 25,85 months. Protein glycosylation, blood mannose concentration and clinical presentation were monitored in everyday clinical practice.

Results
After a mean time period of more than 1 year the majority of patients showed significant improvements in protein glycosylation.

Conclusion
Dietary mannose supplementation shows biological effects in PMM2-CDG patients improving glycosylation in the majority of patients. A double-blind randomized study is needed to examine the role of mannose in the design of a therapy for children with PMM2-CDG in more detail.
Benefits of pulmonary rehabilitation in patients with advanced lymphangioleiomyomatosis (LAM) compared with COPD – a retrospective analysis
Authors: Gloeckl Rainer , Nell Christoph , Schneeberger Tessa , Jarosch Inga , Boensch Martina , Watz Henrik , Wirtz Hubert , Welte Tobias , Kenn Klaus , Koczulla Andreas Rembert 
Published: September 2020

Abstract
Lymphangioleiomyomatosis (LAM) is a rare and progressive cystic lung disease with limited therapeutic options. We retrospectively analyzed the effects of a comprehensive 4-week inpatient pulmonary rehabilitation (PR) program in 58 patients with advanced LAM (FEV1: 45 ± 34%predicted, 6-min walk distance (6MWD): 338 ± 167 m). Exercise performance (6MWD: + 49 ± 50 m; p < 0.001) and quality of life (SF-36 physical component: + 2.4 ± 7.8 points; p = 0.049 and mental component: + 5.2 ± 12.1 points; p < 0.001) increased significantly after PR comparable to an COPD cohort. There were no clinical parameters that predicted changes in outcomes following PR. PR seems to be an effective therapeutic option even in patients with advanced LAM.

Trial registration
Clinical-Trials registration number: NCT04184193; date of registration: December 3, 2019.
Fixed point theorems for nonlinear contractive mappings in ordered b-metric space with auxiliary function
Authors: Seshagiri Rao Namana , Kalyani Karusala , Mitiku Belay 
Published: September 2020

AbstractObjectivesIn this paper we present some fixed point theorems for self mappings satisfying generalized$$(\phi , \psi )$$(ϕ,ψ)-weak contraction condition in partially ordered completeb-metric spaces. The results presented over here generalize and extend some existing results in the literature. Finally, we illustrate two examples to support our results.ResultWe obtained a unique fixed point of a self mapping satisfying certain contraction condition which is involving an auxiliary function. Also, the results are presented for the existence of a common fixed point and a coincidence point for generalized$$(\phi , \psi )$$(ϕ,ψ)-weak contraction mappings in partially ordered completeb-metric space.
Complex dynamics and coexistence of period-doubling and period-halving bifurcations in an integrated pest management model with nonlinear impulsive control
Authors: Li Changtong , Tang Sanyi , Cheke Robert A. 
Published: September 2020

AbstractAn expectation for optimal integrated pest management is that the instantaneous numbers of natural enemies released should depend on the densities of both pest and natural enemy in the field. For this, a generalised predator–prey model with nonlinear impulsive control tactics is proposed and its dynamics is investigated. The threshold conditions for the global stability of the pest-free periodic solution are obtained based on the Floquet theorem and analytic methods. Also, the sufficient conditions for permanence are given. Additionally, the problem of finding a nontrivial periodic solution is confirmed by showing the existence of a nontrivial fixed point of the model’s stroboscopic map determined by a time snapshot equal to the common impulsive period. In order to address the effects of nonlinear pulse control on the dynamics and success of pest control, a predator–prey model incorporating the Holling type II functional response function as an example is investigated. Finally, numerical simulations show that the proposed model has very complex dynamical behaviour, including period-doubling bifurcation, chaotic solutions, chaos crisis, period-halving bifurcations and periodic windows. Moreover, there exists an interesting phenomenon whereby period-doubling bifurcation and period-halving bifurcation always coexist when nonlinear impulsive controls are adopted, which makes the dynamical behaviour of the model more complicated, resulting in difficulties when designing successful pest control strategies.
Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression
Authors: Tao Chengyuan , Li Rong , Xiong Wu , Shen Zongzhuan , Liu Shanshan , Wang Beibei , Ruan Yunze , Geisen Stefan , Shen Qirong , Kowalchuk George A. 
Published: September 2020

AbstractBackgroundPlant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e.bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers.ResultsTo disentangle the mechanism of bio-organic fertilizer action, we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to the following four treatments: bio-organic fertilizer (containingBacillus amyloliquefaciensW19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented withB.amyloliquefaciensW19. We found that sterilized bioorganic fertilizer to whichBacilluswas re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specificPseudomonasspp.. Observed correlations betweenBacillusamendment and indigenousPseudomonasspp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen.ConclusionTogether we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function.
Validity of the dispersion relations in magnetotellurics. Part II: synthetic and field data
Authors: Zorin Nikita , Alekseev Dmitry , Epishkin Dmitrii , Shimizu Hisayoshi , Yakovlev Denis , Zaytsev Sergey 
Published: September 2020

AbstractThe impedance tensor and tipper are shown to be non-causal in some classes of 2-D and 3-D magnetotelluric (MT) models, including those widely encountered off shore. At the same time, examination of a large database of onshore MT records yields only a handful of non-causal tensors, being non-causal due to the influence of nearby artificial conductors rather than some exotic geological conditions. This result implies that the actual chance to encounter a non-causal impedance tensor or tipper in terrestrial MT exploration is vanishingly small, thus securing the universal applicability of the dispersion relation technique for quality assessment of the mentioned transfer functions.
Machine learning helps improve diagnostic ability of subclinical keratoconus using Scheimpflug and OCT imaging modalities
Authors: Shi Ce , Wang Mengyi , Zhu Tiantian , Zhang Ying , Ye Yufeng , Jiang Jun , Chen Sisi , Lu Fan , Shen Meixiao 
Published: September 2020

Abstract
Purpose
To develop an automated classification system using a machine learning classifier to distinguish clinically unaffected eyes in patients with keratoconus from a normal control population based on a combination of Scheimpflug camera images and ultra-high-resolution optical coherence tomography (UHR-OCT) imaging data.

Methods
A total of 121 eyes from 121 participants were classified by 2 cornea experts into 3 groups: normal (50 eyes), with keratoconus (38 eyes) or with subclinical keratoconus (33 eyes). All eyes were imaged with a Scheimpflug camera and UHR-OCT. Corneal morphological features were extracted from the imaging data. A neural network was used to train a model based on these features to distinguish the eyes with subclinical keratoconus from normal eyes. Fisher’s score was used to rank the differentiable power of each feature. The receiver operating characteristic (ROC) curves were calculated to obtain the area under the ROC curves (AUCs).

Results
The developed classification model used to combine all features from the Scheimpflug camera and UHR-OCT dramatically improved the differentiable power to discriminate between normal eyes and eyes with subclinical keratoconus (AUC = 0.93). The variation in the thickness profile within each individual in the corneal epithelium extracted from UHR-OCT imaging ranked the highest in differentiating eyes with subclinical keratoconus from normal eyes.

Conclusion
The automated classification system using machine learning based on the combination of Scheimpflug camera data and UHR-OCT imaging data showed excellent performance in discriminating eyes with subclinical keratoconus from normal eyes. The epithelial features extracted from the OCT images were the most valuable in the discrimination process. This classification system has the potential to improve the differentiable power of subclinical keratoconus and the efficiency of keratoconus screening.
Evaluation of a manualised speech and language therapy programme for children with social communication disorder: the SCIP feasibility study
Authors: Adams Catherine , Gaile Jacqueline , Roddam Hazel , Baxendale Janet , Clitheroe Laura , Emsley Richard 
Published: September 2020

Abstract
Background
Children with Social (Pragmatic) Communication Disorder (SPCD) have long-term needs in using and processing social language and have a high risk of later mental health difficulties. A manualised speech and language therapy programme, the Social Communication Intervention Programme (SCIP) provides therapy content for SPCD. A feasibility study is required to derive more precise estimates of key parameters for a future trial of SCIP.

Aims
To assess the feasibility of conducting a substantive randomized controlled trial of SCIP for children with SPCD.

Methods
A questionnaire was distributed to paediatric speech and language therapists in England. Survey questions addressed number of eligible children, routine intervention provision and trial recruitment factors. In the second phase, a single-arm intervention feasibility study was completed. Fifteen speech and language practitioners identified 24 children aged 5–11 years with SPCD. Practitioners received training/supervision to deliver 20 SCIP therapy sessions to each child. At time 1, parents of participating children provided three communication goals; expected steps in each goal were defined. After intervention, parents and practitioners independently rated each goal compared to baseline ability. Two research practitioners compared parent post-intervention commentaries with outcome scores to derive guidance about clinical significance. All practitioners recorded audio commentaries on therapy experiences. Post-intervention interviews were conducted with 6 practitioners and 6 parents. An expert panel completed a Delphi consultation on trial design.

Results
Routine practice for SPCD varies widely. Children tend to be embedded in autism provision. Participation in a future trial was well supported provided resources are available to services. Outcomes analysis indicated all children except one made some progress on parent ratings; all children made progress on practitioner ratings. A power analysis for a future trial was carried out using current outcome measure as putative primary endpoint. Practitioners’ audio-diaries provided suggestions for training and adaption in a future trial. Outcomes and therapy methods were acceptable to practitioners and parents.

Conclusions
The feasibility study evaluated a novel outcome measure of social communication skills in SPCD. A power calculation indicated a feasible framework for a trial within a realistic period of time. Recommendations for recruitment methods, adaptation of manual and training were supported by practitioners and an expert panel.

Trial registration
Title: Speech-language therapy for child social communication disorder
Trial ID: ISRCTN48030419. Date registered: January 1, 2017. Registered retrospectively.
Maxillary sinus haziness and facial swelling following suction drainage in the maxilla after orthognathic surgery
Authors: Lee Jung-Soo , Kim Moon-Key , Kang Sang-Hoon 
Published: September 2020

Abstract
Background
We investigated the efficacy of a maxillary Jackson-Pratt (J-P) suction drain for preventing maxillary sinus hematoma and facial swelling after maxillary Le Fort I osteotomy (LF1).

Methods
We retrospectively evaluated 66 patients who underwent LF1 at a single institution. Of these, 41 had a J-P suction tube inserted in the mandible and maxilla (maxillary insertion), and 25 had a J-P drain inserted in the mandible only (no maxillary insertion). Facial CT was obtained before and 4 days after surgery. We compared mean midfacial swelling and maxillary sinus haziness by t test and examined correlations between bleeding amount and body mass index (BMI).

Results
For the maxillary-insertion group, the ratio of total maxillary sinus volume to haziness (57.5 ± 24.2%) was significantly lower than in the group without maxillary drain insertion (65.5% ± 20.3; P = .043). This latter group, however, did not have a significantly greater midfacial soft tissue volume (7575 mm3) than the maxillary-insertion group (7250 mm3; P = .728). BMI did not correlate significantly with bleeding amount or facial swelling.

Conclusions
Suction drainage in the maxilla reduced maxillary sinus haziness after orthognathic surgery but did not significantly reduce midfacial swelling.
Identifying pathophysiological bases of disease in COVID-19
Authors: Goldin Carla J. , Vázquez Ramiro , Polack Fernando P. , Alvarez-Paggi Damian 
Published: September 2020

AbstractCOVID-19 is an infectious disease caused by the SARS-CoV-2 virus that can affect lung physiology encompassing a wide spectrum of severities, ranging from asymptomatic and mild symptoms to severe and fatal cases; the latter including massive neutrophil infiltration, stroke and multiple organ failure. Despite many recents findings, a clear mechanistic description underlying symptomatology is lacking.In this article, we thoroughly review the available data involving risk factors, age, gender, comorbidities, symptoms of disease, cellular and molecular mechanisms and the details behind host/pathogen interaction that hints at the existence of different pathophysiological mechanisms of disease. There is clear evidence that, by targeting the angiotensin-converting enzyme II (ACE2) –its natural receptor–, SARS-CoV-2 would mainly affect the renin-angiotensin-aldosterone system (RAAS), whose imbalance triggers diverse symptomatology-associated pathological processes. Downstream actors of the RAAS cascade are identified, and their interaction with risk factors and comorbidities are presented, rationalizing why a specific subgroup of individuals that present already lower ACE2 levels is particularly more susceptible to severe forms of disease. Finally, the notion of endotype discovery in the context of COVID-19 is introduced.We hypothesize that COVID-19, and its associated spectrum of severities, is an umbrella term covering different pathophysiological mechanisms (endotypes). This approach should dramatically accelerate our understanding and treatment of disease(s), enabling further discovery of pathophysiological mechanisms and leading to the identification of specific groups of patients that may benefit from personalized treatments.
Applications of artificial intelligence and deep learning in molecular imaging and radiotherapy
Authors: Arabi Hossein , Zaidi Habib 
Published: September 2020

AbstractThis brief review summarizes the major applications of artificial intelligence (AI), in particular deep learning approaches, in molecular imaging and radiation therapy research. To this end, the applications of artificial intelligence in five generic fields of molecular imaging and radiation therapy, including PET instrumentation design, PET image reconstruction quantification and segmentation, image denoising (low-dose imaging), radiation dosimetry and computer-aided diagnosis, and outcome prediction are discussed. This review sets out to cover briefly the fundamental concepts of AI and deep learning followed by a presentation of seminal achievements and the challenges facing their adoption in clinical setting.