Miracle-dz/UniFAR-FTUs huggingface dataset:
Photo simulation of a river restoration: Relationships between public perception and ecosystem services

Evaluating the ecosystem services (ES) of rivers is a challenging process. We chose to evaluate photo simulations of a river restoration effort using two different approaches. The first approach was an expert evaluation based on the assessment of individual river restoration elements. The second was an evaluation of public perception, which was implemented by collecting 150 respondent replies through an internet questionnaire. Participants in both methods worked with the photo of the original site and three adjusted photos (i.e., with added river restoration elements or recreational amenities). The original photo was taken in Příbor, Czechia, displayed a heavily channelized gravel‐bed river in an urban area. For this reason, the design of the river restoration effort was spatially limited. In the expert evaluation, we obtained an ascending trend; the highest score was achieved by photo simulation which had the highest number of added restoration elements. In the public perception trial, the respondents evaluated the photo simulations based on four ES categories: (a) ecological and hydromorphological function, (b) aesthetics and landscape function, (c) flood protection and (d) recreational function. It was found that the respondents differed original state from the final restoration state in the category (a), (b) and (c). The final state achieved a better score in these categories. The main findings from both approaches were that even a small restoration effort could significantly improve the perception of ES as well as their services itself provided by the restored river. This conclusion could encourage the planning and construction of river restoration projects in even densely inhabited urban areas.
Vector Specific Tolerance Induction for Airwary Gene Therapy

The success of adenoviral mediated airway gene therapy is hindered by host immune responses against adenoviral vectors. Helper-dependent adenoviral vectors (HD-Ad) are devoid of viral coding sequences and have an improved safety profile compared to earlier generation adenoviral vectors. However, intranasal delivery of HD-Ad vectors potentiates a pulmonary adaptive immune response, described in chapter 2, which is a barrier to gene therapy. One of the ways to reduce the immunogenicity of HD-Ad vectors is to increase the efficiency of HD-Ad mediated gene transfer to the airways, which would lessen the immunogen availability, limiting immune response against HD-Ad vectors. In chapter 3, a viral formulation strategy using Nacystelyn and DEAE-Dextran to substantially increase the efficacy of adenoviral mediated gene transfer to the airways is described. To further reduce the immune response to HD-Ad vectors, I have developed two novel strategies to induce vector-specific tolerance. The first strategy, described in chapter 4, involves the use of dendritic cells (DCs) differentiated in presence of IL-10, which are refractory to HD-Ad induced maturation and instead prime generation of regulatory T cells which suppress HD-Ad induced T cell proliferation. Delivery of these DCs pulsed with HD-Ad vectors to mice results in induction of immunological tolerance along with sustained gene expression following multiple rounds of HD-Ad readministrations. The second strategy, described in chapter 5, involves delivery of apoptotic DCs followed by delivery of antigen iii towards which tolerance needs to be generated. Apoptotic DCs are readily taken up by viable DCs, which suppresses DC maturation and induces TGF-β1 secretion, driving generation of regulatory T cells towards the delivered antigen. This strategy has shown remarkable success in achieving tolerance towards ovalbumin. Therefore, these strategies can be used to induce immunological tolerance towards gene therapy vectors which will likely allow for sustained and long term therapeutic transgene expression.
Social structure and reproduction of long-tailed porcupine (Trichys fasciculata)

Abstract We studied the social structure of long-tailed porcupine (Trichys fasciculata) in the tropical rainforest in Sabah, Borneo Island, Malaysia via direct observation assisted by radio-tracking and camera-trapping at burrow entrances. We identified and observed seven individuals in the study area, of which five were radio-tagged. Analysis of their burrow use, home range, and behaviour strongly suggested that five of the observed individuals formed a family group consisting of an adult male–female pair and their three offspring, two of which were born during the study period. The family members used the same burrow site almost every day, and their home ranges largely overlapped. In contrast, the other two individuals never used the burrow sites of this family group. The adult male–female pair was maintained for at least 18 months and reproduced twice during the study period. They had a litter size of one, and the inter-litter interval was estimated to be 11 months. During these two reproductions, the previous litter stayed in the natal family group as a sub-adult after the next juvenile was born. Direct paternal care, such as grooming the juvenile, was also observed. Their low reproductive potential should be considered in conservation efforts.
Automated analysis of foraminifera fossil records by image classification using a convolutional neural network

Abstract. Manual identification of foraminiferal morphospecies or morphotypes under stereo microscopes is time consuming for micropalaeontologists and not possible for nonspecialists. Therefore, a long-term goal has been to automate this process to improve its efficiency and repeatability. Recent advances in computation hardware have seen deep convolutional neural networks emerge as the state-of-the-art technique for image-based automated classification. Here, we describe a method for classifying large foraminifera image sets using convolutional neural networks. Construction of the classifier is demonstrated on the publicly available Endless Forams image set with a best accuracy of approximately 90 %. A complete automatic analysis is performed for benthic species dated to the last deglacial period for a sediment core from the north-eastern Pacific and for planktonic species dated from the present until 180 000 years ago in a core from the western Pacific warm pool. The relative abundances from automatic counting based on more than 500 000 images compare favourably with manual counting, showing the same signal dynamics. Our workflow opens the way to automated palaeoceanographic reconstruction based on computer image analysis and is freely available for use.
Dyeing process and mechanism of eucalyptus veneer with Pterocarpus macrocarpus Kurz heartwood pigment as natural dye

To make full use of the processing residues of Pterocarpus macrocarpus Kurz and reduce the environmental pollution caused by synthetic dyes, natural dye was extracted from Dalbergia bariensis Pierre heartwood. The purpose of the work was to prepare natural dyes of Pterocarpus macrocarpus and identify the key color-producing components to better explore the mechanisms of combination between dyes and eucalyptus veneers. The main components of Pterocarpus macrocarpus heartwood were analyzed by ultra-high performance liquid chromatography with quadrupole-electrostatic field Orbitrap high resolution-mass spectrometry (UPLC-Q-EXACTIVE Orbitrap-MS). The best dyeing process and color fastness were measured. Research technology combining Fourier transform infrared spectroscopy (FTIR) and field emission scanning electron microscopy (FESEM) was used to explore the binding mechanism between eucalyptus veneers and dyestuffs. The UPLC-Q-EXACTIVE Orbitrap-MS results showed 16 flavonoids. The optimal dyeing process parameters of eucalyptus veneer were a 90 °C dyeing temperature, 12 h dyeing time, 4 wt% pigment, and 2 wt% NaCl. The FTIR and FESM results revealed that the dyeing was mainly achieved by physical adsorption and intermolecular hydrogen bonding.
Integrating CBT and CFT within a case formulation approach to reduce depression and anxiety in an older adult with a complex mental and physical health history: a single case study

Abstract Depression and anxiety are major contributors to growing healthcare costs in the UK, particularly with an increasingly ageing population. However, identification of mental health needs in older adults has been overshadowed by a tendency to focus on physical health issues, despite the established co-morbidity of depression, anxiety and physical health conditions. When older adults seek psychological support, treatment options may vary and may be time limited, either because of protocol guidance or due to the resource constraints of psychology services. Time-limited treatment, common in many adult services, may not best meet the needs of older adults, whose physical, cognitive and emotional needs alter with age. It is, therefore, important to identify treatments that best meet the needs of older adults who seek psychological support, but who may arrive with complex mental and physical health histories. This paper aims to explore how a case formulation-driven approach that draws on the theoretical underpinnings of cognitive behavioural therapy (CBT) and compassion-focused therapy (CFT) can be used to reduce anxiety and depression in an older adult with a complex multi-morbid mental and physical health history. This study employs a single-case (A–B) experimental design [assessment (A), CBT and CFT intervention (B)] over 28 sessions. Results suggest the greatest reductions in depression and anxiety (as measured using PHQ-9 and GAD-7) occurred during the CFT phase of the intervention, although scores failed to drop below subclinical levels in any phase of the intervention. This case highlights the value of incorporating CFT with CBT in case formulation-driven interventions. Key learning aims (1) To consider the value of using case formulation approaches in older adult populations. (2) To demonstrate flexibility in balancing evidence-based interventions with service user needs by incorporating CBT and CFT to treat anxiety and depression in an older adult. (3) To present a clinical case to identify how assessment, formulation and treatment of anxiety and depression are adapted to best meet the needs of older adults with complex co-morbid mental and physical health conditions. (4) To appreciate the impact of contextual factors, such as austerity measures, on therapeutic work with individuals with long-standing mental and physical health difficulties.
R2C2: Improving nanopore read accuracy enables the sequencing of highly-multiplexed full-length single-cell cDNA

High-throughput short-read sequencing has revolutionized how transcriptomes are quantified and annotated. However, while Illumina short-read sequencers can be used to analyze entire transcriptomes down to the level of individual splicing events with great accuracy, they fall short of analyzing how these individual events are combined into complete RNA transcript isoforms. Because of this shortfall, long-read sequencing is required to complement short-read sequencing to analyze transcriptomes on the level of full-length RNA transcript isoforms. However, there are issues with both Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) long-read sequencing technologies that prevent their widespread adoption. Briefly, PacBio sequencers produce low numbers of reads with high accuracy, while ONT sequencers produce higher numbers of reads with lower accuracy. Here we introduce and validate a new long-read ONT based sequencing method. At the same cost, our Rolling Circle Amplification to Concatemeric Consensus (R2C2) method generates more accurate reads of full-length RNA transcript isoforms than any other available long-read sequencing method. These reads can then be used to generate isoform-level transcriptomes for both genome annotation and differential expression analysis in bulk or single cell samples. Significance Statement Subtle changes in RNA transcript isoform expression can have dramatic effects on cellular behaviors in both health and disease. As such, comprehensive and quantitative analysis of isoform-level transcriptomes would open an entirely new window into cellular diversity in fields ranging from developmental to cancer biology. The R2C2 method we are presenting here is the first method with sufficient throughput and accuracy to make the comprehensive and quantitative analysis of RNA transcript isoforms in bulk and single cell samples economically feasible.
Online bandwagon effects: Quantitative versus qualitative cues in online comments sections

Bandwagon effects explain an individual’s tendency to conform to and follow other people’s opinions. Drawing on bandwagon effects, this study explored the relative influence of two different bandwagon heuristic cues in an online comments section (quantitative vs qualitative) on changes in news readers’ opinion. Study 1 revealed that qualitative cues have a stronger effect than quantitative cues in changing news readers’ opinions. Study 2 replicated the findings of Study 1 and showed that people change opinions in the same direction as perceived public opinion, providing empirical evidence of online bandwagon effects. The findings offer theoretical insights by explicating the process of opinion change via perceived public opinion as well as practical insights into public opinion formation in online environments.
Comprehensive Genetic Analysis of 128 Candidate Genes in a Cohort With Idiopathic, Severe, or Familial Osteoporosis

Abstract Context The genetic bases of osteoporosis (OP), a disorder with high heritability, are poorly understood at an individual level. Cases of idiopathic or familial OP have long puzzled clinicians as to whether an actionable genetic cause could be identified. Objective We performed a genetic analysis of 28 cases of idiopathic, severe, or familial osteoporosis using targeted massively parallel sequencing. Design Targeted sequencing of 128 candidate genes was performed using Illumina NextSeq. Variants of interest were confirmed by Sanger sequencing or SNP array. Patients and Setting Thirty-seven patients in an academic tertiary hospital participated (54% male; median age, 44 years; 86% with fractures), corresponding to 28 sporadic or familial cases. Main Outcome Measure The identification of rare stop-gain, indel, splice site, copy-number, or nonsynonymous variants altering protein function. Results Altogether, we identified 28 variants of interest, but only 3 were classified as pathogenic or likely pathogenic variants: COL1A2 p.(Arg708Gln), WNT1 p.(Gly169Asp), and IDUA p.(His82Gln). An association of variants in different genes was found in 21% of cases, including a young woman with severe OP bearing WNT1, PLS3, and NOTCH2 variants. Among genes of uncertain significance analyzed, a potential additional line of evidence has arisen for GWAS candidates GPR68 and NBR1, warranting further studies. Conclusions While we hope that continuing efforts to identify genetic predisposition to OP will lead to improved and personalized care in the future, the likelihood of identifying actionable pathogenic variants in intriguing cases of idiopathic or familial osteoporosis is seemingly low.
Acute subjective effects in LSD- and MDMA-assisted psychotherapy

Background: Lysergic acid diethylamide (LSD) and 3,4-methylenedioxymethamphetamine (MDMA) were used in psychotherapy in the 1960s–1980s, and are currently being re-investigated as treatments for several psychiatric disorders. In Switzerland, limited medical use of these substances is possible in patients not responding to other treatments (compassionate use). Methods: This study aimed to describe patient characteristics, treatment indications and acute alterations of mind in patients receiving LSD (100–200 µg) and/or MDMA (100–175 mg) within the Swiss compassionate use programme from 2014–2018. Acute effects were assessed using the 5 Dimensions of Altered States of Consciousness scale and the Mystical Experience Questionnaire, and compared with those in healthy volunteers administered with LSD or MDMA and patients treated alone with LSD in clinical trials. Results: Eighteen patients (including 12 women and six men, aged 29–77 years) were treated in group settings. Indications mostly included posttraumatic stress disorder and major depression. Generally, a drug-assisted session was conducted every 3.5 months after 3–10 psychotherapy sessions. LSD induced pronounced alterations of consciousness on the 5 Dimensions of Altered States of Consciousness scale, and mystical-type experiences with increases in all scales on the Mystical Experience Questionnaire. Effects were largely comparable between patients in the compassionate use programme and patients or healthy subjects treated alone in a research setting. Conclusion: LSD and MDMA are currently used medically in Switzerland mainly in patients with posttraumatic stress disorder and depression in group settings, producing similar acute responses as in research subjects. The data may serve as a basis for further controlled studies of substance-assisted psychotherapy.
Single nucleotide polymorphisms of the complement system C1Q protein in schizophrenia

Schizophrenia is a complex, multifactor psychiatric disorder. Our previous findings indicated that altered functional activity of the complement system, a major mediator of the immune response, is implicated in the pathogenesis of schizophrenia. In the present study single nucleotide polymorphisms (SNPs) of the complement C1q component were investigated in schizophrenia-affected subjects. For this purpose 103 schizophrenics and 105 healthy controls were genotyped for C1q four SNPs (C1qA rs292001, C1qB rs913243, rs291982 and rs631090) using PCR-SSP and Real-time PCR methods. The data obtained indicate no association of C1qA rs292001, C1qB: rs913243, rs631090 polymophisms with schizophrenia whereas the carriers of the C1qB rs291982*T mutant allele were significantly less frequent in patients when compared to control (62% vs 78%, pnomi-nal=0.012, OR=0.456, 95%CI: 0.53-0.91, pcorrected=0.048). The results of the present study suggest the association of C1qB rs291982 polymorphism with schizophrenia. Շիզոֆրենիան բարդ, բազմագործոն բնույթի հոգեկան հիվանդութուն է: Մեր նախորդ հետազոտությունների արդյունքները վկայում են, որ շիզոֆրենիան զուգակցվում է իմունային պատասխանի կարևորագույն միջնորդի` կոմպլեմենտի համակարգի ֆունկցիոնալ ակտիվության խախտմամբ: Տվյալ աշխատանքում ուսումնասիրվել են կոմպլեմենտի C1q բաղադրիչը կոդավորող գենի եզակի նուկլեոտիդային պոլիմորֆիզմները (ԵՆՊ) շիզոֆրենիայով հիվանդների մոտ: Այս նպատակով 103 շիզոֆրենիայով հիվանդների և 105 առողջ անձանց ԴՆԹ-ի նմուշները գենատիպավորվել են C1q-ի չորս ԵՆՊ-երի համար (C1qA: rs292001, C1qB: rs913243, rs291982 և rs631090)` կիրառելով PCR-SSP և Real-time PCR մեթոդները: Համաձայն ստացված տվյալների` C1qA rs292001, C1qB: rs913243 և rs631090 ԵՆՊ-երն ասոցիացված չէին շիզոֆրենիայի հետ, մինչդեռ C1qB rs291982*T մուտանտ ալելի կրողների քանակը զգալիորեն քիչ էր հիվանդների մոտ` առողջ անձանց համեմատությամբ (62% vs 78%, pnominal=0.012, OR=0.456, 95%CI: 0.53-0.91, pcorrected=0.048): Տվյալ հետազոտության արդյունքները վկայում են, որ C1qB rs291982 պոլիմորֆիզմը ասոցիացված է շիզոֆրենիայի հետ: Шизофрения является комплексным психическим заболеванием много-факторной природы. Результаты наших предыдущих исследований свидетельствуют о том, что шизофрения сопровождается нарушением функциональной активности важнейшего медиатора иммунного ответа – системы комплемента. В данной работе исследованы единичные нуклеотидные полиморфизмы (ЕНП) C1q компоненты комплемента у больных шизофренией. С этой целью образцы ДНК 103-х больных шизофренией и 105-ти здоровых лиц были генотипированы по четырем ЕНП C1q (C1qA: rs292001, C1qB: rs913243, rs291982 и rs631090) с помощью методов PCR-SSP и Real-time PCR. Согласно полученным данным, C1qA rs292001, C1qB: rs913243, rs631090 полиморфизмы не ассоциировали с шизофренией, тогда как носителей C1qB rs291982*T мутантной алели среди больных было значительно меньше, чем среди здоровых лиц (62% vs 78%, pnominal=0.012, OR=0.456, 95%CI: 0.53-0.91, pcorrec-ted=0.048). Результаты настоящего исследования свидетельствуют о том, что C1qB rs291982 полиморфизм ассоциирует с шизофренией.
The complete mitochondrial genome of the snakeskin gourami, Trichopodus pectoralis (Regan 1910) (Teleostei: Osphronemidae)

Abstract We sequenced and assembled three whole mitogenome sequences of the commercially important snakeskin gourami Trichopodus pectoralis isolated from Malaysia (introduced), Viet Nam (native) and Thailand (native). The mitogenome length range from 16,397 to 16,420 bp. The final partitioned nucleotide alignment consists of 14,002 bp and supports the monophyly of the genus Trichopodus (95% ultrafast bootstrap support) with T. trichopterus forming a sister group with the members of T. pectoralis.
New Compact Wearable Metamaterials Circular Patch Antennas for IoT, Medical and 5G Applications

The development of compact passive and active wearable circular patch metamaterials antennas for communication, Internet of Things (IoT) and biomedical systems is presented in this paper. Development of compact efficient low-cost wearable antennas are one of the most significant challenges in development of wearable communication, IoT and medical systems. Moreover, the advantage of an integrated compact low-cost feed network is attained by integrating the antenna feed network with the antennas on the same printed board. The efficiency of communication systems may be increased by using efficient passive and active antennas. The system dynamic range may be improved by connecting amplifiers to the printed antenna feed line. Design, design considerations, computed and measured results of wearable circular patch meta-materials antennas with high efficiency for 5G, IoT and biomedical applications are presented in this paper. The circular patch antennas electrical parameters on the human body were analyzed by using commercial full-wave software. The circular patch metamaterial wearable antennas are compact and flexible. The directivity and gain of the antennas with Circular Split-Ring Resonators (CSRR) is higher by 2.5dB to 3dB than the antennas without CSRR. The resonant frequency of the antennas without CSRR is higher by 6% to 9% than the antennas with CSRR. The computed and measured bandwidth of the stacked circular patch wearable antenna with CSRR for IoT and medical applications is around 12%, for S11 lover than −6dB. The gain of the circular patch wearable antenna with CSRR is around 8dBi.