bluuebunny/crossref_metadata_2025 huggingface dataset:
Endogenous drivers of altered immune cell metabolism
Authors: Shanley Lianne C , Fitzgerald Hannah K , O’Rourke Sinead A , Dunne Aisling
Published: December 2022

Dysregulated metabolism has long been recognized as a feature of many metabolic disorders. However, recent studies demonstrating that metabolic reprogramming occurs in immune cells have led to a growing interest in the relationship between metabolic rewiring and immune-mediated disease pathogeneses. It is clear now that immune cell subsets engage in different metabolic pathways depending on their activation and/or maturation state. As a result, it may be possible to modulate metabolic reprogramming for clinical benefit. In this review, we provide an overview of immune cell metabolism with focus on endogenous drivers of metabolic reprogramming given their link to a number of immune-mediated disorders.
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets
Authors: Portik Daniel M. , Brown C. Titus , Pierce-Ward N. Tessa
Published: December 2022

Background

Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic classification and profiling. The development of long-read specific tools for taxonomic classification is accelerating, yet there is a lack of information regarding their relative performance. Here, we perform a critical benchmarking study using 11 methods, including five methods designed specifically for long reads. We applied these tools to several mock community datasets generated using Pacific Biosciences (PacBio) HiFi or Oxford Nanopore Technology sequencing, and evaluated their performance based on read utilization, detection metrics, and relative abundance estimates.

Results

Our results show that long-read classifiers generally performed best. Several short-read classification and profiling methods produced many false positives (particularly at lower abundances), required heavy filtering to achieve acceptable precision (at the cost of reduced recall), and produced inaccurate abundance estimates. By contrast, two long-read methods (BugSeq, MEGAN-LR & DIAMOND) and one generalized method (sourmash) displayed high precision and recall without any filtering required. Furthermore, in the PacBio HiFi datasets these methods detected all species down to the 0.1% abundance level with high precision. Some long-read methods, such as MetaMaps and MMseqs2, required moderate filtering to reduce false positives to resemble the precision and recall of the top-performing methods. We found read quality affected performance for methods relying on protein prediction or exact k-mer matching, and these methods performed better with PacBio HiFi datasets. We also found that long-read datasets with a large proportion of shorter reads (< 2 kb length) resulted in lower precision and worse abundance estimates, relative to length-filtered datasets. Finally, for classification methods, we found that the long-read datasets produced significantly better results than short-read datasets, demonstrating clear advantages for long-read metagenomic sequencing.

Conclusions

Our critical assessment of available methods provides best-practice recommendations for current research using long reads and establishes a baseline for future benchmarking studies.
Transcriptomic analysis reveals the dynamic changes of transcription factors during early development of chicken embryo
Authors: Liao Liqin , Yao Ziqi , Kong Jie , Zhang Xinheng , Li Hongxin , Chen Weiguo , Xie Qingmei
Published: December 2022

Background

The transition from fertilized egg to embryo in chicken requires activation of hundreds of genes that were mostly inactivated before fertilization, which is accompanied with various biological processes. Undoubtedly, transcription factors (TFs) play important roles in regulating the changes in gene expression pattern observed at early development. However, the contribution of TFs during early embryo development of chicken still remains largely unknown that need to be investigated. Therefore, an understanding of the development of vertebrates would be greatly facilitated by study of the dynamic changes in transcription factors during early chicken embryo.

Results

In the current study, we selected five early developmental stages in White Leghorn chicken, gallus gallus, for transcriptome analysis, cover 17,478 genes with about 807 million clean reads of RNA-sequencing. We have compared global gene expression patterns of consecutive stages and noted the differences. Comparative analysis of differentially expressed TFs (FDR < 0.05) profiles between neighboring developmental timepoints revealed significantly enriched biological categories associated with differentiation, development and morphogenesis. We also found that Zf-C2H2, Homeobox and bHLH were three dominant transcription factor families that appeared in early embryogenesis. More importantly, a TFs co-expression network was constructed and 16 critical TFs were identified.

Conclusion

Our findings provide a comprehensive regulatory framework of TFs in chicken early embryo, revealing new insights into alterations of chicken embryonic TF expression and broadening better understanding of TF function in chicken embryogenesis.
Patient-reported outcomes in individuals with advanced gastrointestinal stromal tumor treated with ripretinib in the fourth-line setting: analysis from the phase 3 INVICTUS trial
Authors: Schöffski Patrick , George Suzanne , Heinrich Michael C. , Zalcberg John R. , Bauer Sebastian , Gelderblom Hans , Serrano César , Jones Robin L. , Attia Steven , D’Amato Gina , Chi Ping , Reichardt Peter , Becker Claus , Shi Kelvin , Meade Julie , Ruiz-Soto Rodrigo , Blay Jean-Yves , von Mehren Margaret
Published: December 2022

Background

Ripretinib is a novel switch-control kinase inhibitor that inhibits KIT and PDGFRA signaling. In the INVICTUS phase 3 trial, ripretinib increased median progression-free survival and prolonged overall survival vs. placebo in ≥ fourth-line advanced GIST. Here, we report prespecified analysis of quality of life (QoL) as assessed by patient-reported outcome (PRO) measures and an exploratory analysis evaluating the impact of alopecia on QoL.

Methods

In the INVICTUS trial (NCT03353753), QoL was assessed using the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-C30; physical function, role function, overall health, and overall QoL) and the EuroQoL 5-Dimension 5-Level (EQ-5D-5 L; visual analogue scale). Analysis of covariance (ANCOVA) models compared changes in scores from baseline to treatment cycle 2, day 1 within and between ripretinib and placebo. Within the ripretinib arm, repeated measures models assessed the impact of alopecia on QoL.

Results

Patients receiving ripretinib maintained QoL (as assessed by the EORTC QLQ-C30 and EQ-5D-5 L PRO measures) from baseline to cycle 2, day 1 whereas QoL declined with placebo, resulting in clinically significant differences between treatments (nominal P < 0.01). The most common treatment-emergent adverse event with ripretinib was alopecia; however, QoL was similarly maintained out to treatment cycle 10, day 1 in patients receiving ripretinib who developed alopecia and those who did not.

Conclusion

PRO assessments in the INVICTUS trial suggest that patients on ripretinib maintain their QoL out to C2D1, unlike patients receiving placebo. Longitudinal QoL was maintained for patients receiving ripretinib out to cycle 10, day 1 (approximately 8 months; past the point of median progression-free survival with ripretinib [6.3 months]), even if the patients developed alopecia.

Trial registration

ClinicalTrials.gov Identifier: NCT03353753; first posted: November 27, 2017.
Impact of coronavirus disease 2019 on the number of newly diagnosed cancer patients and examinations and surgeries performed for cancer in Japan: a nationwide study
Authors: Terashima Takeshi , Konishi Hiroshi , Sato Yasunori , Igarashi Muneki , Yanagibashi Takafumi , Konno Ryo , Saya Hideyuki , Doki Yuichiro , Kakizoe Tadao
Published: December 2022

Background

The coronavirus disease 2019 (COVID-19) pandemic has rapidly and dramatically influenced healthcare across Japan. However, the influence of the COVID-19 pandemic on the number of newly diagnosed cancer, surgical treatment, and diagnostic examination for cancer types have not been completely investigated all over Japan. This study aimed to analyze the number of cases before and during the COVID-19 pandemic.

Methods

This retrospective study was a survey that asked to provide the number of cases diagnosed with gastric, colorectal, lung, breast, and cervical cancer between January 2019 and December 2020. The survey was sent to tertiary healthcare hospitals, including national cancer institutions, university hospitals, and general hospitals, all over Japan. Data obtained from 105 of 486 surveyed hospitals were evaluated, and the number of cases in each quarter in 2020 was compared with that in the equivalent quarter in 2019.

Results

In the second quarter (Q2), significant reductions were observed in the median number of newly diagnosed cases from 2019 to 2020: gastric cancer, 26.7% (43 vs. 32, p <  0.001); colorectal cancer, 17.9% (52 vs. 40, p <  0.001); lung cancer, 12.3% (53.5 vs. 47, p <  0.001); and breast cancer, 13.1% (43 vs. 35.5, p <  0.001). A significant reduction of 11.4% (9 vs. 8, p = 0.03) was observed in the third quarter (Q3) for cervical cancer. In Q2, the number of cases decreased by 30.9% (25 vs. 15, p <  0.001) for stage I gastric cancer, by 27.3% (12 vs. 9, p <  0.001) for stage I colorectal cancer, and by 17.6% (13 vs. 10, p <  0.001) for stage II breast cancer. The magnitude of reduction was significant for the localized stages of gastric, colorectal, and breast cancer according to diagnostic examinations in Q2 and surgical and endoscopic treatment in Q3 rather than that for lung or cervical cancer.

Conclusions

COVID-19 has prolonged collateral effects on cancer care, including examination, diagnosis, and surgery, with significant effects on gastric cancer, followed by colorectal, lung, breast, and cervical cancer in Japan.
Pneumatic tourniquet versus no tourniquet in transfemoral amputation – a study protocol for a randomized controlled trial
Authors: Brix Anna Trier Heiberg , Nymark Tine , Schmal Hagen , Lindberg-Larsen Martin
Published: December 2022

Background

Lower extremity amputation patients represent a frail group with extensive comorbidity. Transfemoral amputation is a high-risk procedure with 37–50% risk of mortality in the first year. Substantial blood loss during surgery increases the risk of anemic complications and death for these already weakened patients. The use of tourniquet during surgery may reduce blood loss, the need for blood transfusions, the related complications as well as the length of the surgery. However the use of tourniquet may be related to impaired wound healing and hence the use should be investigated in a randomized controlled trial.

The primary aim of this study is to investigate the total blood loss and secondary to investigate differences in complications after transfemoral amputation between patients operated with or without tourniquet.

Methods

The total blood loss is calculated using Nadlers approach. Based on data from a pilot series, the sample size was calculated to 124, allocated 1:1 in two groups of 62 participants to ensure detection of at least 200 mL difference in the total blood loss. The primary outcome is the total blood loss. Secondary outcomes are blood transfusions, duration of surgery, length of hospital stay and risk of complications within 90 days (re-admissions, re-operations and mortality). Explorative outcomes are 1 year mortality and re-operation risk. Further explorative outcomes are postoperative quality of life (questionnaire EQ-5D-5L) and evaluation of number of prosthesis users including evaluation of prosthesis-specific function measured 3, 6, and 12 months postoperatively.

Discussion

The possibility to enhance patient safety is highly relevant and this trial will provide data for evidence based recommendations of best practice in amputation surgery.

Trial registration

The trial is registered on ClinicalTrials.gov with ID: NCT05550623. Initial release: 13/09 2022.
Protective effect of silymarin on tacrolimus-induced kidney and liver toxicity
Authors: Terzi Funda , Ciftci Mustafa Kemal
Published: December 2022

Background

Tacrolimus (FK506) is an immunosuppressive agent and has toxic side effects such as nephrotoxicity, hepatotoxicity, and neurotoxicity. In our study, we aimed to investigate the protective effect of silymarin on renal and hepatic toxicity considered to be tacrolimus related.

Methods

In this 6-week experimental study, 46 eight-week-old healthy male rats were used. The groups comprised the Control (healthy rats, n = 6), Tac (tacrolimus 1 mg/kg, n = 8), silymarin 100 mg/kg (SLI 100 mg/kg n = 8), Tac + SLI 100 (tacrolimus 1 mg/kg + SLI 100 n = 8), SLI 200 (SLI 200 mg/kg n = 8), and Tac + SLI 200 (tacrolimus 1 mg/kg + SLI 200 mg/kg n = 8). After 6 weeks, all rats were sacrificed, and the tissue follow-up procedure was performed for kidney and liver tissues, histopathology, and in situ TUNEL analysis. Blood samples were analyzed for the total antioxidant capacity (TAC), total oxidant capacity (TOC), alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyl transferase (GGT), albumin, total bilirubin, creatine.

Results

Histopathological findings of kidney and liver tissue of rats were determined to increase statistically in Tac group compared to SLI 1 00 and SLI 200 groups (P < 0.05). In addition, the Tac + SLI 100 and Tac + SLI 200 groups were found to be statistically similar to the Control group (P > 0.05). The in situ TUNEL method showed that the tacrolimus increased apoptosis while the silymarin decreased it. TOC levels increased statistically in Tac groups compared to silymarin-treated groups (P < 0.05). Although the TAC level was not statistically significant among the experimental groups (P > 0.05), the lowest was measured in the Tac group. The ALT, AST, GGT, total bilirubin, and creatine values were higher in the Tac group than in the silymarin groups (P < 0.05). There was no statistically significant difference between the groups with regard to the albumin level (P > 0.05).

Conclusion

In our study, we determined that tacrolimus caused damage to kidney and liver tissue. Histopathological, biochemical and apoptotic findings show that silymarin has a protective effect against nephrotoxicity and hepatotoxicity caused by tacrolimus.
Clinical features of Kawasaki disease initially mimicking retropharyngeal abscess: a retrospective analysis
Authors: Chen Yong-chao , Pan Hong-guang , Jia De-sheng , Wang Hao-cheng , Li Lan , Teng Yi-shu
Published: December 2022

Objective

Incomplete Kawasaki disease (IKD) initially presenting as retropharyngeal abnormality is very rare and is prone to misdiagnosis and missed diagnosis, often leading to poor prognosis. Most patients were misdiagnosed with retropharyngeal abscesses. Here, we describe and compare IKD patients initially presenting with retropharyngeal abnormalities, typical KD patients without retropharyngeal abnormalities and retropharyngeal abscess patients.

Methods

We performed a retrospective case–control study comparing IKD patients initially presenting with retropharyngeal abnormalities to both KD patients without retropharyngeal abnormalities and retropharyngeal abscess patients admitted to Shenzhen Children’s Hospital between January 2016 and December 2021.

Results

We evaluated data from 10 IKD patients initially presenting with retropharyngeal abnormalities (Group A), 20 typical KD patients (Group B) and 16 surgical drainage confirmed retropharyngeal abscess patients (Group C). Compared to Group B, we observed that Group A was older and had a more intense inflammatory response. On the day of admission, Groups A and C had similar early clinical presentations, and there were no significant differences in any major signs or symptoms. Close observation for the development of new KD signs and symptoms and unresponsiveness to empirical antibiotic therapy after 3 days is extremely important. The CRP (p = 0.011), AST (p = 0.002) and ALT (p = 0.013) levels were significantly higher and the WBC (P = 0.040) levels were significantly lower in Group A than in Group C. Neck radiological findings, such as the presence of ring enhancement (p = 0.001) and mass effects on the airway, are also useful tools for distinguishing these two diseases.

Conclusion

The careful observation of the signs and symptoms of this disease and the comprehensive analysis of the laboratory tests and neck radiological findings may help clinicians become aware of retropharyngeal abnormality as an atypical presentation of KD. Then, unnecessary treatments could be reduced, and the occurrence of serious complications can be avoided.
Distance learning during the COVID-19 pandemic for children with ADHD and/or ASD: a European multi-center study examining the role of executive function deficits and age
Authors: Thorell Lisa B. , Fuermaier Anselm B. M. , Christiansen Hanna , Steinmayr Ricarda , Baeyens Dieter , de la Peña Almudena Giménez , Groom Madeleine J. , Idrees Iman , van der Oord Saskia , van den Hoofdakker Barbara J. , Luman Marjolein , Mammarella Irene C. , Skoglund Charlotte
Published: December 2022

Background

One of the COVID-19 pandemic consequences that has affected families the most is school lockdowns. Some studies have shown that distance learning has been especially challenging for families with a child with neurodevelopmental disorders such as ADHD or ASD. However, previous studies have not taken the heterogeneity of these disorders into account. The aim of the present study was therefore to investigate differences between families with a child with ADHD, ASD, or both conditions, and to examine the role of underlying deficits in executive functioning (EF) in both children and parents in relation to negative and positive effects of distance learning.

Methods

Survey data assessing both negative and positive experiences of distance learning were collected from parents with a child aged 5–19 years in seven Western European countries: the UK, Germany, Spain, Sweden, the Netherlands, Italy, and Belgium. Altogether, the study included 1010 families with a child with ADHD and/or ASD and an equally large comparison group of families with a child without mental health problems. We included measures of three different types of negative effects (i.e., effects on the child, effects on the parent, and lack of support from school) and positive effects on the family.

Results

Results confirmed that families with a child with ADHD, ASD or a combination of ADHD and ASD showed higher levels of both negative and positive effects of distance learning than the comparison group. However, few differences were found between the clinical groups. Group differences were more pronounced for older compared to younger children. Regarding the role of both ADHD/ASD diagnosis and EF deficits, primarily children’s EF deficits contributed to high levels of negative effects. Parent EF deficits did not contribute significantly beyond the influence of child EF deficits. Families of children with ADHD/ASD without EF deficits experienced the highest levels of positive effects.

Conclusions

School closings during COVID-19 have a major impact on children with EF problems, including children with neurodevelopmental disorders. The present study emphasizes that schools should not focus primarily on whether a student has a neurodevelopmental disorder, but rather provide support based on the student’s individual profile of underlying neuropsychological deficits.
The effect of biomechanical foot‐based interventions on patellofemoral joint loads during gait in adults with and without patellofemoral pain or osteoarthritis: a systematic review protocol
Authors: Kayll Samual A. , Hinman Rana S. , Bennell Kim L. , Bryant Adam L. , Rowe Patrick L. , Paterson Kade L.
Published: December 2022

Background

Patellofemoral pain is highly prevalent across the lifespan, and a significant proportion of people report unfavourable outcomes years after diagnosis. Previous research has implicated patellofemoral joint loading during gait in patellofemoral pain and its sequelae, patellofemoral osteoarthritis. Biomechanical foot‐based interventions (e.g., footwear, insoles, orthotics, taping or bracing) can alter patellofemoral joint loads by reducing motions at the foot that increase compression between the patella and underlying femur via coupling mechanisms, making them a promising treatment option. This systematic review will summarise the evidence about the effect of biomechanical foot‐based interventions on patellofemoral joint loads during gait in adults with and without patellofemoral pain and osteoarthritis.

Methods

MEDLINE (Ovid), the Cumulative Index to Nursing and Allied Health Literature CINAHL, The Cochrane Central Register of Controlled Trials (CENTRAL), SPORTdiscus (EBSCO) and Embase (Ovid) will be searched. Our search strategy will include terms related to ‘patellofemoral joint’, ‘loads' and ‘biomechanical foot‐based interventions'. We will include studies published in the English language that assess the effect of biomechanical foot‐based interventions on patellofemoral joint loads, quantified by patellofemoral joint pressure, patellofemoral joint reaction force and/or knee flexion moment. Two reviewers will independently screen titles and abstracts, complete full‐text reviews, and extract data from included studies. Two reviewers will assess study quality using the Revised Cochrane Risk of Bias (RoB 2) tool or the Cochrane Risk Of Bias In Non‐Randomized Studies – of Interventions (ROBINS‐I) tool. We will provide a synthesis of the included studies' characteristics and results. If three or more studies are sufficiently similar in population and intervention, we will pool the data to conduct a meta‐analysis and report findings as standardised mean differences with 95% confidence intervals. If a meta‐analysis cannot be performed, we will conduct a narrative synthesis of the results and produce forest plots for individual studies.

Discussion

This protocol outlines the methods of a systematic review that will determine the effect of biomechanical foot‐based interventions on patellofemoral joint loads. Our findings will inform clinical practice by identifying biomechanical foot‐based interventions that reduce or increase patellofemoral joint loads, which may aid the treatment of adults with patellofemoral pain and osteoarthritis.

Trial registration

Registered with PROSPERO on the 4th of May 2022 (CRD42022315207).
A novel computed tomography angiography technique: guided preoperative localization and design of anterolateral thigh perforator flap
Authors: Yu Xin-xin , Yang Shi-feng , Ji Cong-shan , Qiu Shen-qiang , Qi Yao-dong , Wang Xi-ming
Published: December 2022

Background

Anterolateral thigh perforator (ALTP) flap is considered a versatile flap for soft tissue reconstruction. Computed tomography angiography (CTA) is used for mapping perforator in abdominal-based reconstruction; however, it is less commonly used in ALTP due to its poor imaging efficacy. In this study, we introduced a novel CTA technique for preoperative localization and design of ALTP flap and evaluated its value in directing surgical reconstruction.

Results

Thirty-five patients with soft tissue defects were consecutively enrolled. Modified CTA procedures, such as sharp convolution kernel, ADMIRE iterative reconstruction, 80 kV tube voltage, high flow contrast agent and cinematic rendering image reconstruction, were used to map ALTPs. A total of 287 perforators (including 884 sub-branches) were determined, with a mean of 5 perforators per thigh (range 2–11). The ALTPs were mainly concentrated in the “hot zone” (42%, 121/287) or the distal zone (41%, 118/287). Most perforators originated from the descending branch of the lateral circumflex femoral artery (76%, 219/287). Three perforator types, namely musculocutaneous (62%, 177/287), septocutaneous (33%, 96/287), and mixed pattern (5%, 14/287), were identified. The median pedicle length measured by two methods was 4.1 cm (range 0.7–20.3 cm) and 17.0 cm (range 4.7–33.9 cm), respectively, and the median diameter of the skin flap nourished by one perforator was 3.4 cm (IQR 2.1–5.7 cm). Twenty-eight ALTP flaps were obtained with the guidance of CTA, and 26 flaps survived after follow-up.

Conclusions

The proposed CTA mapping technique is a useful tool for preoperative localization and design of ALTP flap.
Comparison of a deep learning-accelerated T2-weighted turbo spin echo sequence and its conventional counterpart for female pelvic MRI: reduced acquisition times and improved image quality
Authors: Ren Jing , Li Yuan , Liu Fei-Shi , Liu Chong , Zhu Jin-Xia , Nickel Marcel Dominik , Wang Xiao-Ye , Liu Xin-Yu , Zhao Jia , He Yong-Lan , Jin Zheng-Yu , Xue Hua-Dan
Published: December 2022

Objectives

To investigate the feasibility of a deep learning-accelerated T2-weighted turbo spin echo (TSE) sequence (T2DL) applied to female pelvic MRI, using standard T2-weighted TSE (T2S) as reference.

Methods

In total, 24 volunteers and 48 consecutive patients with benign uterine diseases were enrolled. Patients in the menstrual phase were excluded. T2S and T2DL sequences in three planes were performed for each participant. Quantitative image evaluation was conducted by calculating the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR). Image geometric distortion was evaluated by measuring the diameters in all three directions of the uterus and lesions. Qualitative image evaluation including overall image quality, artifacts, boundary sharpness of the uterine zonal layers, and lesion conspicuity were assessed by three radiologists using a 5-point Likert scale, with 5 indicating the best quality. Comparative analyses were conducted for the two sequences.

Results

T2DL resulted in a 62.7% timing reduction (1:54 min for T2DL and 5:06 min for T2S in axial, sagittal, and coronal imaging, respectively). Compared to T2S, T2DL had significantly higher SNR (p ≤ 0.001) and CNR (p ≤ 0.007), and without geometric distortion (p = 0.925–0.981). Inter-observer agreement regarding qualitative evaluation was excellent (Kendall’s W > 0.75). T2DL provided superior image quality (all p < 0.001), boundary sharpness of the uterine zonal layers (all p < 0.001), lesion conspicuity (p = 0.002, p < 0.001, and p = 0.021), and fewer artifacts (all p < 0.001) in sagittal, axial, and coronal imaging.

Conclusions

Compared with standard TSE, deep learning-accelerated T2-weighted TSE is feasible to reduce acquisition time of female pelvic MRI with significant improvement of image quality.
On some variational inequality-constrained control problems
Authors: Treanţă Savin , Antczak Tadeusz , Saeed Tareq
Published: December 2022

In this paper, by considering some properties associated with scalar functionals of multiple-integral type, we study the well-posedness and generalized well-posedness for a new variational inequality-constrained optimization problems By using the set of approximating solutions, we state some characterization theorems on well-posedness and generalized well-posedness. Also, in order to validate the derived results, some examples are given.
The community ecology perspective of omics data
Authors: Jurburg Stephanie D. , Buscot François , Chatzinotas Antonis , Chaudhari Narendrakumar M. , Clark Adam T. , Garbowski Magda , Grenié Matthias , Hom Erik F. Y. , Karakoç Canan , Marr Susanne , Neumann Steffen , Tarkka Mika , van Dam Nicole M. , Weinhold Alexander , Heintz-Buschart Anna
Published: December 2022

The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement ofɑ- andβ-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data.
From concept to validation of a wireless environmental sensor for the integral application of preventive conservation methodologies in low-budget museums
Authors: Laborda Jaime , García-Castillo Ana María , Mercado Ricardo , Peiró-Vitoria Andrea , Perles Angel
Published: December 2022

The effective implementation of preventive conservation strategies requires tools to continuously measure the environmental conditions to which the cultural objects are exposed. In this sense, the European Horizon 2020 project CollectionCare aims to provide an affordable preventive conservation service for individual objects focused to small museums with limited budgets. Although the use of data loggers has been a must in the past, new deployments tend to use wired and wireless sensors that provide real-time information and the ability to instantly analyse the data, allowing immediate action to be taken in the event of a threat towards a cultural object. For already constructed buildings, wireless systems have the advantage that, a priori, deployments are simpler, faster and cheaper, but have to deal with complex heritage environments with long distances to be covered and very thick walls to cross. In many cases, commercial systems of this type are not economically viable for small museums with limited budgets. Moreover, conservators who try to approach such solutions are often overwhelmed by unclear technical specifications that do not allow them to determine whether the solution fits their environment or not, giving rise to great frustration. Among others, the CollectionCare includes the design of a specific low-cost wireless sensor, being the aim of this article to present to both technical and non-technical readers, the design choices made regarding the housing, attachment method, power source, wireless transmission technique and selection of the environmental sensors following European standards. Also, the effective implementation of the device in three stages to prove the concep until to get a near-production version is presented. The developed device has been deployed in museums in Belgium, Italy, Greece, Latvia, Denmark and Spain, and the validation results are presented, showing that it is feasible to have a cost-effective proposal that it is easy to install and configure and can operate for 10 years without the need for maintenance or battery replacement except if it is needed to comply with annual recalibration if standards such as ISO 11799:2015 are required.
New types of investments needed to address barriers to scaling up wildfire risk mitigation
Authors: Yung Laurie , Gray Benjamin J. , Wyborn Carina , Miller Brett Alan , Williams Daniel R. , Essen Maureen
Published: December 2022

Background

Wildfire mitigation is becoming increasingly urgent, but despite the availability of mitigation tools, such as prescribed fire, managed wildfire, and mechanical thinning, the USA has been unable to scale up mitigation. Limited agency capacity, inability to work across jurisdictions, lack of public support, and procedural delays have all been cited as barriers to mitigation. But in the context of limited resources and increasing urgency, how should agencies prioritize investments to address these barriers?

Results

To better understand different investments for scaling up mitigation, we examined how the wildfire problem is framed, building on existing social science demonstrating that agency approaches depend in part on how problems are framed. Using national-level policy documents and in-depth interviews, we found three ways of framing the barriers to scaling up mitigation, each emphasizing certain aspects of the problem and prioritizing different solutions or investments. The first framing, the Usual Suspects, focused on inadequate resources, cumbersome procedural requirements, delays due to litigation, and lack of public support. The solutions—to increase funding, streamline NEPA, limit litigation, and educate the public—suggest that more resources and fewer restrictions will enable agencies to scale up mitigation. The second framing, Agency-Agency Partnerships, focused on the ways that organizational structure and capacity constrain the development of effective cross-boundary collaboration. Here solutions prioritized organizational changes and capacity building to enable agencies to navigate different missions and build trust in order to develop shared priorities. The third framing, Engaging the Public, focused on lack of public support for mitigation, the need for meaningful public engagement and multi-stakeholder collaboration, and investments to build support to scale up mitigation.

Conclusions

This analysis reveals that investing in collaborative capacity to advance agency-agency partnerships and public engagement might not slow down mitigation, but rather enable agencies to “go slow to go fast” by building the support and mechanisms necessary to increase the pace and scale of mitigation work. Reframing the wildfire problem through a careful analysis of competing frames and the underlying assumptions that privilege particular solutions can reveal a broader suite of solutions that address the range of key barriers.
Hobbes and the Political Economy of Population
Authors: Smith Brian
Published: December 2022

This article argues that Hobbes was actively engaged in the debates about population size as a component of his broader approach to political economy. By the seventeenth century, beliefs about economic well-being routinely turned back onto the question of population size. This article situates Hobbes's arguments about populations in and among the common arguments for the movement of people in the seventeenth century. Hobbes rejected the natural law tradition of hospitality, which required that states take care of foreigners, and populationist arguments, which assumed that economic progress was predicated on rapid population growth. Specifically, this article will show that Hobbes held a view common to the late Tudor period; namely, a wise sovereign should be actively engaged in regulating population inflows and outflows. Not only did this require careful management of domestic procreative policies, but it also had implications for colonization and war-making.
Balbach and Brunner: A Missing Stop on the Road from Warburton to Friedman-Meiselman and St. Louis
Authors: Belongia Michael T. , Ireland Peter N.
Published: December 2022

“The Relative Stability of Monetary Velocity and the Investment Multiplier in the United States, 1897–1958,” by Milton Friedman and David Meiselman (1963), typically is recognized as the original study that used a reduced-form equation to evaluate whether autonomous expenditures or the quantity of money was the dominant influence on aggregate spending. It also provided the foundation for the better-known St. Louis equation that followed. Missing from this evolution, however, are important precedents by Karl Brunner and Anatol Balbach that also employed a reduced-form framework to offer evidence on the same debate between the Keynesian expenditure theory and the quantity theory of money. Moreover, these authors also investigated whether the demand-for-money function was stable and inversely related to an interest rate, properties necessary in their reasoning before any more general model of national income determination could be developed. With this foundation, Balbach, in his 1963 PhD dissertation, then derived a reduced-form expression for personal income from an explicit theoretical model and, in its estimation, anticipated and addressed some of the empirical criticisms later directed at the work by Friedman and Meiselman and the early versions of the St. Louis equation. Taken together, the theoretical and empirical work reported in Balbach's dissertation and in a 1959 article by Brunner and Balbach suggest these papers are clear antecedents of later reduced-form expressions and should be recognized as such.
Gustav Schmoller and the Institutional Context of Entrepreneurship
Authors: Störring Matthias
Published: December 2022

Given the growing call for the restoration of the place of entrepreneurship in economic theory, familiarity with the works of Gustav Schmoller would be a great asset for a better understanding of the nature of the enterprise and the role of entrepreneurs. This article examines Schmoller's still-underutilized research, which makes him one of the founding fathers of research in entrepreneurship. It illustrates Schmoller's distinct contextual perspective on entrepreneurship. The most compelling notion is the emphasis on and accentuation of the modern enterprise as a special form of institution that can be characterized by three dimensions: (1) the macroscopic dimension refers to the enterprise as a unitary corporate actor, (2) the microscopic dimension encompasses the organizational structure of the enterprise, and (3) the metascopic dimension describes the institutional link between the organization and society. These three dimensions also shape Schmoller's “psychological-ethical” idea of the entrepreneur as an economic and social actor.
On John Bates Clark's “Naive Productivity Ethics”: A Note
Authors: Fiorito Luca , Vatiero Massimiliano
Published: December 2022

This article explores in detail the reactions among American economists to John Bates Clark's famously controversial claim that the marginal productivity theory of factor pricing and distribution is necessarily just. The general debate around Clark's “naïve productivity ethics,” as George Stigler sharply called it, transcended the then existing distinctions within the discipline and involved figures of virtually all theoretical and ideological persuasions—from prolabor progressives such as Richard T. Ely to staunch conservatives such as Thomas Nixon Carver. Our reconstruction reveals that, contrary to several standard historical accounts, for American early twentieth-century marginalism, let alone American economics at large, Clark's solution to the ethical problem of distributive justice was far more divisive than consolidating.
Associação entre IDEB, gastos com pessoal próprio e compras no ensino fundamental dos municípios paulistas
Authors: Crozatti Jaime , Mandu dos Santos Gabriela
Published: December 2022

A partir do fortalecimento de relações entre a gestão pública e o setor privado, como característica contemporânea das mudanças no setor público, o objetivo deste trabalho é analisar o nível de associação entre o Índice de Desenvolvimento da Educação Básica (IDEB) e os gastos com pessoal próprio e com compras de materiais e serviços de terceiros dos municípios paulistas, agregados em dois grupos: A) os que privilegiaram os recursos da educação fundamental, com a aplicação de 60% ou mais em remuneração de pessoal próprio; e B) os que privilegiaram os gastos em compras de materiais e serviços de terceiros, com a aplicação de menos de 60% dos recursos na remuneração do pessoal próprio, no período de 2008 a 2018. Com os dados do Tribunal de Contas do Estado de São Paulo e do Instituto Nacional de Ensino e Pesquisa Anísio Teixeira, as análises descritivas e de regressão multivariada mostram que os 433 municípios que concentraram os gastos com a educação fundamental na remuneração do pessoal próprio apresentaram significativo e alto nível de associação estatística entre os gastos na educação fundamental e o IDEB; os 211 municípios que os concentraram na compra de materiais e serviços de terceiros não mostraram associação com significância estatística entre os mesmos gastos e o IDEB. Estes resultados indicam que há significativa quantidade de municípios paulistas com relevantes gastos públicos com compras de materiais e serviços de terceiros da educação fundamental, para os quais tais gastos não se mostram consistentes com a política educacional e os resultados apresentados em indicadores como o IDEB.
Discriminação de gênero e políticas públicas e corporativas de combate ao assédio sexual nas relações de emprego
Authors: Cavalcanti Boucinhas Filho Jorge , De Mello Rezende Colnago Lorena
Published: December 2022

O assédio sexual constitui uma discriminação de gênero. A maioria de suas ocorrências envolve agressor homem e vítima mulher. Na maioria delas a solicitação de participação em uma atividade sexual decorre da condição feminina, que motivou desejos sexuais em seu superior ou colega. O fato de a leis penais e trabalhistas não fazerem nenhum recorte de gênero para a prática do assédio sexual permite que em situações concretas assediadoras mulheres sejam punidas criminalmente, dispensadas por justa causa e condenadas a reparar a vítima, seja ela homem ou mulher. Permite também que assediadores homens sejam punidos nessas três esferas ao assediarem outro homem. No entanto, uma política eficaz de combate ao assédio sexual pressupõe que se reconheça que o assédio sexual é uma forma de discriminação de gênero e, portanto, de violência de gênero. Sem essa consciência, as políticas públicas e corporativas destinadas a erradicar essa chaga jamais terão êxito.
O Retorno do Rei: As origens desagradáveis do direito administrativo
Authors: Lawson Gary
Published: December 2022

Is Administrative Law Unlawful?, de Philip Hamburger, é um livro realmente brilhante e importante. Nesse prodigioso estudo, o professor Hamburger desvenda os antecedentes do direito britânico e civil do direito administrativo americano moderno, mostrando que o direito administrativo contemporâneo “é realmente apenas a manifestação mais recente de um problema recorrente”. Esse problema é o problema do poder: suas tentações, seus perigos e sua tendência a corromper. O direito administrativo, longe de ser um produto distinto da modernidade, é assim a “expressão contemporânea da velha tendência para o poder absoluto — para o poder consolidado fora e acima da lei”. Ele representa precisamente as formas de ação governamental que o constitucionalismo — tanto em geral quanto como manifestado especificamente na Constituição dos Estados Unidos — foi criado para prevenir. Assim, praticamente todos os aspectos do direito administrativo moderno desafiam diretamente a Constituição.
Esse livro extraordinário será imensamente valioso para qualquer pessoa interessada no direito público. Meus comentários aqui dizem respeito a dois pontos relativamente menores que exigem mais esclarecimentos. Primeiro, o professor Hamburger não identifica claramente o que ser “ilegal” significa para o direito administrativo. Significa “em violação à Constituição escrita”? “Em violação às normas constitucionais não escritas?” “Em violação ao direito natural?” Há evidências de que o professor Hamburger quer dizer algo mais do que violar a Constituição escrita, mas não está claro o que mais se pretende. A fim de avaliar o verdadeiro status do direito administrativo, devemos ter uma concepção mais direta da lei do que a que o professor Hamburger nos fornece.
Em segundo lugar, grande parte da análise histórica e constitucional do professor Hamburger se concentra na subdelegação da autoridade legislativa. Embora sua discussão contenha inúmeros insights profundos, incluindo alguns que requerem corrigir meu próprio aprendizado anterior sobre o assunto, ela não discute como distinguir a interpretação dos agentes judiciais e executivos da elaboração de leis por esses agentes. Presumidamente, a proibição da subdelegação da autoridade legislativa proíbe apenas esta última. Descobrir onde a interpretação termina e onde começa a legislação é uma das questões mais difíceis em toda a jurisprudência, e não estou convencido de que o professor Hamburger consiga obter com sucesso uma conclusão em torno dela.
Mas essas são apenas modestas tentativas de buscar defeitos em uma obra inovadora que deve manter pessoas de diferentes convicções engajadas e ocupadas por muito tempo.
Decadência da autotutela administrativa: a proteção do ato administrativo e de seus efeitos jurídicos
Authors: Marques Neto Floriano de Azevedo , Zago Marina Fontão
Published: December 2022

É inerente ao próprio conceito de ato administrativo a produção de efeitos jurídicos. Como, então, a autotutela — e, mais especificamente, a decadência da autotutela — impacta os efeitos gerados pelo ato administrativo em questão? O presente artigo defende que os efeitos jurídicos de um ato administrativo que se prolongam no tempo estão abarcados pelo instituto da decadência da autotutela e, assim, se devem ser preservados. Para isso, analisa os fundamentos da decadência da autotutela administrativa, como mecanismo estabilizador das relações sociais e concretizador da segurança jurídica, e delineia a lógica pela qual devem-se preservar os próprios efeitos do ato administrativo em questão. Em seguida, aplica essas considerações para um caso abstrato (porém bastante prático): o reequilíbrio econômico-financeiro de um contrato de concessão por meio de aumento tarifário. No caso, o reequilíbrio é contado a partir do reconhecimento do desequilíbrio financeiro; decorrido tal prazo, o aumento tarifário deverá ser preservado, conjuntamente com o ato em si que reconheceu o desequilíbrio.
O papel do princípio da indisponibilidade do interesse público na Administração Pública consensual
Authors: Faria Luzardo
Published: December 2022

A consensualidade já se firmou como uma realidade inquestionável do direito administrativo brasileiro contemporâneo. Nesse contexto, porém, verifica-se, na doutrina, na atividade administrativa e na prática forense, discussões a respeito de uma suposta incompatibilidade entre os instrumentos consensuais da administração pública e o tradicional princípio da indisponibilidade do interesse público. O presente artigo  objetiva analisar qual é o papel que ainda pode ser exercido pelo princípio da indisponibilidade no paradigma da administração pública consensual. Após identificar o que se considera falhas cometidas pelos dois lados deste polarizado debate, objetiva-se demonstrar por que o interesse público pode ser atingido por meio de pactos consensuais da administração pública com particulares e também como essas relações devem ser firmadas para que sejam válidas de acordo com o referido princípio. Ao final, conclui-se pela existência de seis parâmetros de validade que devem ser observados pelas decisões administrativas consensuais: legalidade, isonomia, publicidade, motivação, moralidade e segurança jurídica.