Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Burkholderia cepacia strains that express a Burkholderia pseudomallei-like capsular polysaccharide

ABSTRACT Burkholderia pseudomallei and Burkholderia cepacia are Gram-negative, soil-dwelling bacteria that are found in a wide variety of environmental niches. While B. pseudomallei is the causative agent of melioidosis in humans and animals, members of the B. cepacia complex typically only cause disease in immunocompromised hosts. In this study, we report the identification of B. cepacia strains isolated from either patients or soil in Laos and Thailand that express a B. pseudomallei-like 6-deoxyheptan capsular polysaccharide (CPS). These B. cepacia strains were initially identified based on their positive reactivity in a latex agglutination assay that uses the CPS-specific monoclonal antibody (mAb) 4B11. Mass spectrometry and recA sequencing confirmed the identity of these isolates as B. cepacia (formerly genomovar I). Total carbohydrates extracted from B. cepacia cell pellets reacted with B. pseudomallei CPS-specific mAbs MCA147, 3C5, and 4C4, but did not react with the B. pseudomallei lipopolysaccharide-specific mAb Pp-PS-W. Whole genome sequencing of the B. cepacia isolates revealed the presence of genes demonstrating significant homology to those comprising the B. pseudomallei CPS biosynthetic gene cluster. Collectively, our results provide compelling evidence that B. cepacia strains expressing the same CPS as B. pseudomallei co-exist in the environment alongside B. pseudomallei. Since CPS is a target that is often used for presumptive identification of B. pseudomallei, it is possible that the occurrence of these unique B. cepacia strains may complicate the diagnosis of melioidosis. IMPORTANCE Burkholderia pseudomallei, the etiologic agent of melioidosis, is an important cause of morbidity and mortality in tropical and subtropical regions worldwide. The 6-deoxyheptan capsular polysaccharide (CPS) expressed by this bacterial pathogen is a promising target antigen that is useful for rapidly diagnosing melioidosis. Using assays incorporating CPS-specific monoclonal antibodies, we identified both clinical and environmental isolates of Burkholderia cepacia that express the same CPS antigen as B. pseudomallei. Because of this, it is important that staff working in melioidosis-endemic areas are aware that these strains co-exist in the same niches as B. pseudomallei and do not solely rely on CPS-based assays such as latex-agglutination, AMD Plus Rapid Tests, or immunofluorescence tests for the definitive identification of B. pseudomallei isolates.
Resistance, mechanism, and fitness cost of specific bacteriophages for Pseudomonas aeruginosa

ABSTRACT The bacteriophage is an effective adjunct to existing antibiotic therapy; however, in the course of bacteriophage therapy, host bacteria will develop resistance to bacteriophages, thus affecting the efficacy. Therefore, it is important to describe how bacteria evade bacteriophage attack and the consequences of the biological changes that accompany the development of bacteriophage resistance before the bacteriophage is applied. The specific bacteriophage vB3530 of Pseudomonas aeruginosa (P. aeruginosa) has stable biological characteristics, short incubation period, strong in vitro cleavage ability, and absence of virulence or resistance genes. Ten bacteriophage-resistant strains (TL3780-R) were induced using the secondary infection approach, and the plaque assay showed that vB3530 was less sensitive to TL3780-R. Identification of bacteriophage adsorption receptors showed that the bacterial surface polysaccharide was probably the adsorption receptor of vB3530. In contrast to the TL3780 parental strain, TL3780-R is characterized by the absence of long lipopolysaccharide chains, which may be caused by base insertion of wzy or deletion of galU. It is also intriguing to observe that, in comparison to the parent strain, the bacteriophage-resistant strains TL3780-R mostly exhibited a large cost of fitness (growth rate, biofilm formation, motility, and ability to produce enhanced pyocyanin). In addition, TL3780-R9 showed increased susceptibility to aminoglycosides and chlorhexidine, which may be connected to the loss and down-regulation of mexX expression. Consequently, these findings fully depicted the resistance mechanism of P. aeruginosa to vB3530 and the fitness cost of bacteriophage resistance, laying a foundation for further application of bacteriophage therapy. IMPORTANCE The bacteriophage is an effective adjunct to existing antibiotic therapy; However, bacteria also develop defensive mechanisms against bacteriophage attack. Thus, there is an urgent need to deeply understand the resistance mechanism of bacteria to bacteriophages and the fitness cost of bacteriophage resistance so as to lay the foundation for subsequent application of the phage. In this study, a specific bacteriophage vB3530 of P. aeruginosa had stable biological characteristics, short incubation period, strong in vitro cleavage ability, and absence of virulence or resistance genes. In addition, we found that P. aeruginosa may lead to phage resistance due to the deletion of galU and the base insertion of wzy, involved in the synthesis of lipopolysaccharides. Simultaneously, we showed the association with the biological state of the bacteria after bacteria acquire bacteriophage resistance, which is extremely relevant to guide the future application of therapeutic bacteriophages.
Structural geology of the Rub' Al‐Khali Basin, Saudi Arabia

The Rub' Al‐Khali basin lies below a Quaternary sand sea, and the structural evolution from the Late Precambrian to Neogene is known only from reflection seismic, gravity, and magnetic data, and wells. Gravity and magnetic data show north‐south and northwest‐southeast trends, matching mapped Precambrian faults. The deepest structures imaged on reflection seismic data are undrilled Precambrian rifts filled with layered strata at depths up to 13 km. The distribution of Ediacaran‐Cambrian Ara/Hormuz mobile salt is restricted to an embayment in the eastern Rub' Al‐Khali. The Precambrian rifts show local inversion and were peneplained at base Phanerozoic. A broad crustal‐scale fold (Qatar Arch) developed in the Carboniferous and amplified in the Late Triassic, separating subbasins in the west and east Rub' Al‐Khali. A phase of kilometer‐scale folding occurred in the Late Cretaceous, coeval with thrusting and ophiolite obduction in eastern Oman. These folds trend predominantly north‐south, oblique to the northwesterly shortening direction, and occasionally have steep fault zones close to their axial surfaces. The trend and location of these folds closely matches the Precambrian lineaments identified in this study, demonstrating preferential reactivation of basement structures. Compression along the Zagros suture reactivated these folds in the Neogene, this time the result of highly oblique, north‐northeast to south‐southwest shortening. Cretaceous‐Tertiary fold style is interpreted as transpression with minor strain partitioning. Permian, Jurassic, and Eocene evaporite horizons played no role in the structural evolution of the basin, but the Eocene evaporites caused widespread kilometer‐scale dissolution collapse structures in the basin center.
Barriers to use of interpreters in outpatient mental health care: Exploring the attitudes of psychotherapists

The support of professional interpreters is an essential component of adequate mental health care for migrants with limited language proficiency. Nevertheless, for varied reasons, only a small proportion of outpatient psychotherapists provide interpreter-mediated psychotherapy for migrants. This study explored the perspectives of psychotherapists who have not worked with professional interpreters in outpatient mental health care to identify factors that may prevent the use of interpreters in outpatient care and explore possible incentives to provide interpreter-mediated psychotherapy for migrants with limited language proficiency. Semi-structured interviews were conducted with 13 outpatient psychotherapists in Northern Germany who had not yet worked with professional interpreters in outpatient care. The interviews were audio recorded, transcribed and analysed using a structured content analysis approach. The psychotherapists named structural as well as subjective barriers and concerns. Findings suggest that improving structural factors, such as secure funding, minimal additional work, better preparation and training could facilitate the integration of professional interpreters into everyday treatment. Psychotherapists also mentioned concerns about their own confidence (e.g., insecurities regarding the triadic situation), the patient (e.g., reduced openness), the interpreter (e.g., doubts about suitability, motivation and empathy), as well as the therapeutic process (e.g., unclear allocation of roles). However, positive aspects and opportunities of interpreter-mediated psychotherapy were also described. These could be enhanced by the presence of conducive factors, such as existing trust between all parties and professional cooperation between interpreter and psychotherapist.
User Requirements in Developing a Novel Dietary Assessment Tool for Children: Mixed Methods Study

Background The prevalence of childhood obesity and comorbidities is rising alarmingly, and diet is an important modifiable determinant. Numerous dietary interventions in children have been developed to reduce childhood obesity and overweight rates, but their long-term effects are unsatisfactory. Stakeholders call for more personalized approaches, which require detailed dietary intake data. In the case of primary school children, caregivers are key to providing such dietary information. However, as school-aged children are not under the full supervision of one specific caregiver anymore, data are likely to be biased. Recent technological advancements provide opportunities for the role of children themselves, which would serve the overall quality of the obtained dietary data. Objective This study aims to conduct a child-centered exploratory sequential mixed methods study to identify user requirements for a dietary assessment tool for children aged 5 to 6 years. Methods Formative, nonsystematic narrative literature research was undertaken to delineate initial user requirements and inform prototype ideation in an expert panel workshop (n=11). This yielded 3 prototype dietary assessment tools: FoodBear (tangible piggy bank), myBear (smartphone or tablet app), and FoodCam (physical camera). All 3 prototypes were tested for usability by means of a usability task (video analyses) and user experience (This or That method) among 14 Dutch children aged 5 to 6 years (n=8, 57% boys and n=6, 43% girls). Results Most children were able to complete FoodBear’s (11/14, 79%), myBear’s (10/14, 71%), and FoodCam’s (9/14, 64%) usability tasks, but all children required assistance (14/14, 100%) and most of the children encountered usability problems (13/14, 93%). Usability issues were related to food group categorization and recognition, frustrations owing to unsatisfactory functioning of (parts) of the prototypes, recall of food products, and the distinction between eating moments. No short-term differences in product preference between the 3 prototypes were observed, but autonomy, challenge, gaming elements, being tablet based, appearance, social elements, and time frame were identified as determinants of liking the product. Conclusions Our results suggest that children can play a complementary role in dietary data collection to enhance the data collected by their parents. Incorporation of a training program, auditory or visual prompts, reminders and feedback, a user-friendly and intuitive interaction design, child-friendly food groups or icons, and room for children’s autonomy were identified as requirements for the future development of a novel and usable dietary assessment tool for children aged 5 to 6 years. Our findings can serve as valuable guidance for ongoing innovations in the field of children’s dietary assessment and the provision of personalized dietary support.
Carbon Monoxide-releasing Antibacterial Molecules Target Respiration and Global Transcriptional Regulators*

Carbon monoxide, a classical respiratory inhibitor, also exerts vasodilatory, anti-inflammatory, and antiapoptotic effects. CO-releasing molecules have therapeutic value, increasing phagocytosis and reducing sepsis-induced lethality. Here we identify for the first time the bacterial targets of Ru(CO)3Cl(glycinate) (CORM-3), a ruthenium-based carbonyl that liberates CO rapidly under physiological conditions. Contrary to the expectation that CO would be preferentially inhibitory at low oxygen tensions or anaerobically, Escherichia coli cultures were also sensitive to CORM-3 at concentrations equimolar with oxygen. CORM-3, assayed as ruthenium, was taken up by bacteria and rapidly delivered CO intracellularly to terminal oxidases. Microarray analysis of CORM-3-treated cells revealed extensively modified gene expression, notably down-regulation of genes encoding key aerobic respiratory complexes. Genes involved in metal metabolism, homeostasis, or transport were also differentially expressed, and free intracellular zinc levels were elevated. Probabilistic modeling of transcriptomic data identified the global transcription regulators ArcA, CRP, Fis, FNR, Fur, BaeR, CpxR, and IHF as targets and potential CO sensors. Our discovery that CORM-3 is an effective inhibitor and global regulator of gene expression, especially under aerobic conditions, has important implications for administration of CO-releasing agents in sepsis and inflammation.
Prostigmatid soil mites of alfalfa fields in Northwest of Iran (East Azerbaijan Province) with one genus, subgenus and four species as new records.

ABSTRACT: Prostigmatic soil mite fauna of alfalfa fields of six regions in Northwest of Iran (East Azerbaijan) including Soofian, Payam, Zenooz, Marand, Shabestar and Jolfa was studied at three different times of the year 2006 (mid-May, mid-July and mid-September), based on Nested design. In this study 24 species, 26 genera and 17 families belonging to 8 superfamilies were identified in which 1 genus and 1 species were new records for mite fauna of Iran and 4 genera and 4 species were new records for mite fauna of east Azerbaijan province. Results showed that the maximum mean number was obtained in Shabestar at mid-September. This study confirms that at the case of high temperature and low humidity, the diversity and frequency of mites are increased.
Example‐Based Colourization Via Dense Encoding Pyramids

We propose a novel deep example‐based image colourization method called dense encoding pyramid network. In our study, we define the colourization as a multinomial classification problem. Given a greyscale image and a reference image, the proposed network leverages large‐scale data and then predicts colours by analysing the colour distribution of the reference image. We design the network as a pyramid structure in order to exploit the inherent multi‐scale, pyramidal hierarchy of colour representations. Between two adjacent levels, we propose a hierarchical decoder–encoder filter to pass the colour distributions from the lower level to higher level in order to take both semantic information and fine details into account during the colourization process. Within the network, a novel parallel residual dense block is proposed to effectively extract the local–global context of the colour representations by widening the network. Several experiments, as well as a user study, are conducted to evaluate the performance of our network against state‐of‐the‐art colourization methods. Experimental results show that our network is able to generate colourful, semantically correct and visually pleasant colour images. In addition, unlike fully automatic colourization that produces fixed colour images, the reference image of our network is flexible; both natural images and simple colour palettes can be used to guide the colourization.
Sexual behaviours and risk with women in MSM in sub-Saharan Africa

In sub-Saharan Africa (SSA), MSM – a high HIV prevalence group – experience strong social stigma and pressure to have female partners. Accordingly, they could constitute a bridging group for HIV transmission to cisgender women. We developed a multilevel summary of MSM sexual behaviors and risk with women in various SSA regions. Following PRISMA guidelines, we conducted a mixed-method systematic review of data of sex with women in MSM in SSA. We performed meta-analyses on quantitative data (i.e. percent of recent sex and condomless sex with women) for each SSA region (when proportions reported in ≥4 studies). Pooled proportions were calculated using random-effects models. Qualitative data were analyzed using the three-step thematic synthesis methodology. The pooled proportion of MSM who had sex with women was 58% (33–83%) in East Africa (in the previous 3 months), and 27% (13–48%) in Southern Africa and 50% (95% CI 39–62%) in West Africa (in the previous 6 months); 23% (16–32%) of MSM in West Africa had condomless sex with a woman (during the most recent encounter). Approximately one quarter of MSM had recent multiple female partners. MSM reported having sex with women because of heteronormative pressure, erotic/romantic attraction, or financial needs leading to transactional sex. MSM may act as a bridging population to women in SSA, as they commonly practice sex with women and risky sexual behaviors with them. HIV programmes and community-based support for MSM should be adapted to this population to reduce this risk.
Direct and indirect associations of experience of racial discrimination, dietary patterns and obesity in adults from southern Brazil

Objective: To analyse the direct and indirect associations of experience of racial discrimination on dietary patterns (DP), obesity and abdominal obesity. Design: This is a cross-sectional population-based study. The main exposure was self-reported experiences of racial discrimination (Experiences of Discrimination scale). The mediator variables were the DP: healthy, Brazilian traditional, sugar and carbohydrates, and fast food. The outcomes were obesity (BMI ≥ 30 kg/m2) and abdominal obesity (waist circumference ≥ 88 cm for women; ≥ 102 cm for men). Structural equation modelling was applied. Setting: Porto Alegre, Brazil. Participants: Totally, 400 adults aged between 20 and 70 years were participated. Results: The mean age of participants was 47·2 years (s d = 13·9), and 75 % were women. Experiencing racial discrimination had a positive direct effect on obesity (healthy DP: β = 0·153, P < 0·05; Brazilian DP: β = 0·156, P < 0·05; sugar and carbohydrates DP: β = 0·156, P < 0·05; and fast-food DP: β = 0·153, P < 0·05) and abdominal obesity (healthy DP: β = 0·206, P < 0·01; Brazilian DP: β = 0·210, P < 0·01; sugar and carbohydrates DP: β = 0·204, P < 0·01; and fast-food DP: β = 0·204, P < 0·01). The experience of racial discrimination did not have a direct effect on DP, nor did it exert an indirect effect on obesity and abdominal obesity through any DP. Conclusions: A higher experience of racial discrimination is associated with obesity and abdominal obesity, independent of diet.
PirateNets: Physics-informed Deep Learning with Residual Adaptive Networks

While physics-informed neural networks (PINNs) have become a popular deep learning framework for tackling forward and inverse problems governed by partial differential equations (PDEs), their performance is known to degrade when larger and deeper neural network architectures are employed. Our study identifies that the root of this counter-intuitive behavior lies in the use of multi-layer perceptron (MLP) architectures with non-suitable initialization schemes, which result in poor trainablity for the network derivatives, and ultimately lead to an unstable minimization of the PDE residual loss. To address this, we introduce Physics-informed Residual Adaptive Networks (PirateNets), a novel architecture that is designed to facilitate stable and efficient training of deep PINN models. PirateNets leverage a novel adaptive residual connection, which allows the networks to be initialized as shallow networks that progressively deepen during training. We also show that the proposed initialization scheme allows us to encode appropriate inductive biases corresponding to a given PDE system into the network architecture. We provide comprehensive empirical evidence showing that PirateNets are easier to optimize and can gain accuracy from considerably increased depth, ultimately achieving state-of-the-art results across various benchmarks. All code and data accompanying this manuscript will be made publicly available at \url{https://github.com/PredictiveIntelligenceLab/jaxpi}.
Regression-Based Proximal Causal Inference

In observational studies, identification of causal effects is threatened by the potential for unmeasured confounding. Negative controls have become widely used to evaluate the presence of potential unmeasured confounding thus enhancing credibility of reported causal effect estimates. Going beyond simply testing for residual confounding, proximal causal inference (PCI) was recently developed to debias causal effect estimates subject to confounding by hidden factors, by leveraging a pair of negative control variables, also known as treatment and outcome confounding proxies. While formal statistical inference has been developed for PCI, these methods can be challenging to implement in practice as they involve solving complex integral equations that are typically ill-posed. In this paper, we develop a regression-based PCI approach, employing a two-stage regression via familiar generalized linear models to implement the PCI framework, which completely obviates the need to solve difficult integral equations. In the first stage, one fits a generalized linear model (GLM) for the outcome confounding proxy in terms of the treatment confounding proxy and the primary treatment. In the second stage, one fits a GLM for the primary outcome in terms of the primary treatment, using the predicted value of the first-stage regression model as a regressor which as we establish accounts for any residual confounding for which the proxies are relevant. The proposed approach has merit in that (i) it is applicable to continuous, count, and binary outcomes cases, making it relevant to a wide range of real-world applications, and (ii) it is easy to implement using off-the-shelf software for GLMs. We establish the statistical properties of regression-based PCI and illustrate their performance in both synthetic and real-world empirical applications.
RESPONSE OF GROUNDNUT (Arachis hypogaea L.) TO RHIZOBIA INOCULATION, NITROGEN AND PHOSPHORUS FERTILIZERS ON AN ALFISOL IN THE NORTHERN GUINEA SAVANNA OF NIGERIA

ix Table of Content. xi List of Tables. xvi List of Figures. xvii List of Appendices. xviii CHAPTER ONE. 1 1.0INTRODUCTION. 1 1.1Background . 1 1.2 Statement of Research Problem. 4 1.3 Justification. 5 1.4 Aims and Objectives. 6 CHAPTER TWO. 7 2.0 LITERATURE REVIEW. 7 2.1 Importance of Groundnuts. 7 2.2 Groundnut Production in Nigeria. 8