High Sensitivity Cryogenic Temperature Sensors Based on Arc-Induced Long-Period Fiber Gratings.

In this paper, we investigated the evolution of the dispersion curves of long-period fiber gratings (LPFGs) from room temperature down to 0 K. We considered gratings arc-induced in the SMF28 fiber and in two B/Ge co-doped fibers. Computer simulations were performed based on previously published experimental data. We found that the dispersion curves belonging to the lowest-order cladding modes are the most affected by the temperature changes, but those changes are minute when considering cladding modes with dispersion turning points (DTP) in the telecommunication windows. The temperature sensitivity is higher for gratings inscribed in the B/Ge co-doped fibers near DTP and the optimum grating period can be chosen at room temperature. A temperature sensitivity as high as -850 pm/K can be obtained in the 100-200 K temperature range, while a value of -170 pm/K is reachable at 20 K.

A Simple Optical Sensor Based on Multimodal Interference Superimposed on Additive Manufacturing for Diameter Measurement.

In many areas, the analysis of a cylindrical structure is necessary, and a form to analyze it is by evaluating the diameter changes. Some areas can be cited: pipelines for oil or gas distribution and radial growth of trees whose diameter changes are directly related to irrigation and the radial expansion since it depends on the water soil deficit. For some species, these radial variations can change in around 5 mm. This paper proposes and experimentally investigates a sensor based on a core diameter mismatch technique for diameter changes measurement. The sensor structure is a combination of a cylindrical piece developed using a 3D printer and a Mach-Zehnder interferometer. The pieces were developed to assist in monitoring the diameter variation. It is formed by splicing an uncoated short section of MMF (Multimode Fiber) between two standard SMFs (Singlemode Fibers) called SMF-MMF-SMF (SMS), where the MMF length is 15 mm. The work is divided into two main parts. Firstly, the sensor was fixed at two points on the first developed piece, and the diameter reduction caused dips or peaks shift of the transmittance spectrum due to curvature and strain influence. The fixation point (FP) distances used are: 5 mm, 10 mm, and 15 mm. Finally, the setup with the best sensitivity was chosen, from first results, to develop another test with an optimization. This optimization is performed in the printed piece where two supports are created so that only the strain influences the sensor. The results showed good sensitivity, reasonable dynamic range, and easy setup reproduction. Therefore, the sensor could be used for diameter variation measurement for proposed applications.

Optical Strain Gauge Prototype Based on a High Sensitivity Balloon-like Interferometer and Additive Manufacturing.

An optical strain gauge based on a balloon-like interferometer structure formed by a bent standard single-mode fiber combined with a 3D printer piece has been presented and demonstrated, which can be used to measure displacement. The interferometer has a simple and compact size, easy fabrication, low cost, and is repeatable. The sensor is based on the interference between the core and cladding modes. This is caused by the fiber's curvature because when light propagates through the curved balloon-shaped interferometer region, a portion of it will be released from the core limitation and coupled to the cladding. The balloon has an axial displacement as a result of how the artwork was constructed. The sensor head is sandwiched between two cantilevers such that when there is a displacement, the dimension associated with the micro bend is altered. The sensor response as a function of displacement can be determined using wavelength shift or intensity change interrogation techniques. Therefore, this optical strain gauge is a good option for applications where structure displacement needs to be examined. The sensor presents a sensitivity of 55.014 nm for displacement measurements ranging from 0 to 10 mm and a strain sensitivity of 500.13 pm/µÏµ.

Optical Fiber Interferometers Based on Arc-Induced Long Period Gratings at INESC TEC.

In this work, we review the most important achievements of an INESC TEC long-period-grating-based fiber optic Michelson and Mach-Zehnder configuration modal interferometer with coherence addressing and heterodyne interrogation as a sensing structure for measuring environmental refractive index and temperature. The theory for Long Period Grating (LPG) interferometers and coherence addressing and heterodyne interrogation is presented. To increase the sensitivity to external refractive index and temperature, several LPG interferometers parameters are studied, including order of cladding mode, a reduction of the fiber diameter, different type of fiber, cavity length and the antisymmetric nature of cladding modes.

Arc-Induced Long-Period Fiber Gratings at INESC TEC. Part II: Properties and Applications in Optical Communications and Sensing.

In this work, we review the most important achievements of INESC TEC related to the properties and applications of arc-induced long-period fiber gratings. The polarization dependence loss, the spectral behavior at temperatures ranging from cryogenic up to 1200 °C and under exposure to ultraviolet and gamma radiation is described. The dependence of gratings sensitivity on the fabrication parameters is discussed. Several applications in optical communications and sensing domains are referred.

Arc-Induced Long-Period Fiber Gratings at INESC TEC. Part I: Fabrication, Characterization and Mechanisms of Formation.

In this work, we reviewed the most important achievements of INESC TEC related to the fabrication of long-period fiber gratings using the electric arc technique. We focused on the fabrication setup, the type of fiber used, and the effect of the fabrication parameters on the gratings' transmission spectra. The theory was presented, as well as a discussion on the mechanisms responsible for the formation of the gratings, supported by the measurement of the temperature reached by the fiber during an electric arc discharge.

Simulation of the Transmission Spectrum of Long-Period Fiber Gratings Structures with a Propagating Acoustic Shock Front.

In this paper, we investigate modification of transmission spectra of long-period fiber grating structures with an acoustic shock front propagating along the fiber. We simulate transmission through inhomogeneous long-period fiber gratings, π-shift and reflective π-shift gratings deformed by an acoustic shock front. Coupled mode equations describing interaction of co-propagating modes in a long-period fiber grating structures with inhomogeneous deformation are used for the simulation. Two types of apodization are considered for the grating modulation amplitude, such as uniform and raised-cosine. We demonstrate how the transmission spectrum is produced by interference between the core and cladding modes coupled at several parts of the gratings having different periods. For the π-shift long-period fiber grating having split spectral notch, the gap between the two dips becomes several times wider in the grating with the acoustic wave front than the gap in the unstrained grating. The behavior of reflective long-period fiber gratings depends on the magnitude of the phase shift near the reflective surface: an additional dip is formed in the 0-shift grating and the short-wavelength dip disappears in the π-shift grating.

Whole genome sequence of Mycobacterium kansasii isolates of the genotype 1 from Brazilian patients with pulmonary disease demonstrates considerable heterogeneity.

Mycobacterium kansasii is an opportunistic pathogen and one of the most commonly encountered species in individuals with lung disease. We here report the complete genome sequence of 12 clinical isolates of M. kansasii from patients with pulmonary disease in Brazil.

Multilocus sequence typing scheme versus pulsed-field gel electrophoresis for typing Mycobacterium abscessus isolates.

Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus.

Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features.

Transcription termination is a crucial step in the production of conforming mRNAs and functional proteins. Under cellular stress conditions, the transcription machinery fails to identify the termination site and continues transcribing beyond gene boundaries, a phenomenon designated as transcription readthrough. However, the prevalence and impact of this phenomenon in healthy human tissues remain unexplored. Here, we assessed transcription readthrough in almost 3000 transcriptome profiles representing 23 human tissues and found that 34% of the expressed protein-coding genes produced readthrough transcripts. The production of readthrough transcripts was restricted in genomic regions with high transcriptional activity and was associated with inefficient splicing and increased chromatin accessibility in terminal regions. In addition, we showed that these transcripts contained several binding sites for the same miRNA, unravelling a potential role as miRNA sponges. Overall, this work provides evidence that transcription readthrough is pervasive and non-stochastic, not only in abnormal conditions but also in healthy tissues. This suggests a potential role for such transcripts in modulating normal cellular functions.

SRRM2 splicing factor modulates cell fate in early development.

Embryo development is an orchestrated process that relies on tight regulation of gene expression to guide cell differentiation and fate decisions. The Srrm2 splicing factor has recently been implicated in developmental disorders and diseases, but its role in early mammalian development remains unexplored. Here, we show that Srrm2 dosage is critical for maintaining embryonic stem cell pluripotency and cell identity. Srrm2 heterozygosity promotes loss of stemness, characterised by the coexistence of cells expressing naive and formative pluripotency markers, together with extensive changes in gene expression, including genes regulated by serum-response transcription factor (SRF) and differentiation-related genes. Depletion of Srrm2 by RNA interference in embryonic stem cells shows that the earliest effects of Srrm2 heterozygosity are specific alternative splicing events on a small number of genes, followed by expression changes in metabolism and differentiation-related genes. Our findings unveil molecular and cellular roles of Srrm2 in stemness and lineage commitment, shedding light on the roles of splicing regulators in early embryogenesis, developmental diseases and tumorigenesis.

Genetic Characterization and Population Structure of Drug-Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing.

The present study aimed to determine the genetic diversity of isolates of Mycobacterium tuberculosis (Mtb) from presumed drug-resistant tuberculosis patients from several states of Brazil. The isolates had been submitted to conventional drug susceptibility testing for first- and second-line drugs. Multidrug-resistant (MDR-TB) (54.8%) was the most frequent phenotypic resistance profile, in addition to an important high frequency of pre-extensive resistance (p-XDR-TB) (9.2%). Using whole-genome sequencing (WGS), we characterized 298 Mtb isolates from Brazil. Besides the analysis of genotype distribution and possible correlations between molecular and clinical data, we determined the performance of an in-house WGS pipeline with other online pipelines for Mtb lineages and drug resistance profile definitions. Sub-lineage 4.3 (52%) was the most frequent genotype, and the genomic approach revealed a p-XDR-TB level of 22.5%. We detected twenty novel mutations in three resistance genes, and six of these were observed in eight phenotypically resistant isolates. A cluster analysis of 170 isolates showed that 43.5% of the TB patients belonged to 24 genomic clusters, suggesting considerable ongoing transmission of DR-TB, including two interstate transmissions. The in-house WGS pipeline showed the best overall performance in drug resistance prediction, presenting the best accuracy values for five of the nine drugs tested. Significant associations were observed between suffering from fatal disease and genotypic p-XDR-TB (p = 0.03) and either phenotypic (p = 0.006) or genotypic (p = 0.0007) ethambutol resistance. The use of WGS analysis improved our understanding of the population structure of MTBC in Brazil and the genetic and clinical data correlations and demonstrated its utility for surveillance efforts regarding the spread of DR-TB, hopefully helping to avoid the emergence of even more resistant strains and to reduce TB incidence and mortality rates.

Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species.

Species belonging to the Mycobacterium kansasii complex (MKC) are frequently isolated from humans and the environment and can cause serious diseases. The most common MKC infections are caused by the species M. kansasii (sensu stricto), leading to tuberculosis-like disease. However, a broad spectrum of virulence, antimicrobial resistance and pathogenicity of these non-tuberculous mycobacteria (NTM) are observed across the MKC. Many genomic aspects of the MKC that relate to these broad phenotypes are not well elucidated. Here, we performed genomic analyses from a collection of 665 MKC strains, isolated from environmental, animal and human sources. We inferred the MKC pangenome, mobilome, resistome, virulome and defence systems and show that the MKC species harbours unique and shared genomic signatures. High frequency of presence of prophages and different types of defence systems were observed. We found that the M. kansasii species splits into four lineages, of which three are lowly represented and mainly in Brazil, while one lineage is dominant and globally spread. Moreover, we show that four sub-lineages of this most distributed M. kansasii lineage emerged during the twentieth century. Further analysis of the M. kansasii genomes revealed almost 300 regions of difference contributing to genomic diversity, as well as fixed mutations that may explain the M. kansasii's increased virulence and drug resistance.

Mycobacterium fragae sp. nov., a non-chromogenic species isolated from human respiratory specimens.

Three isolates of a slow-growing, non-chromogenic mycobacterium were grown from three sputum samples of a patient from the north-eastern Ceará state in Brazil. Identification at species level could not be obtained with PCR restriction analysis of the hsp65 gene. In order to characterize the isolates we carried out phenotypic and genotypic tests. We sequenced the nearly complete 16S rRNA gene and obtained partial sequences of the hsp65 (encoding the hypervariable region of the 65 kDa heat-shock protein) and rpoB (encoding the beta-subunit of RNA polymerase) genes. The three isolates turned out to be identical and most closely related to the species Mycobacterium celatum and Mycobacterium kyorinense. The results, however, showed significant differences between these species and the isolates studied, which led us to consider them members of a novel species for which we propose the name Mycobacterium fragae. The type strain is HF8705(T) ( = Fiocruz-INCQS/CMRVS P4051(T) = DSM 45731(T)).

Nontuberculous mycobacteria in respiratory samples from patients with pulmonary tuberculosis in the state of Rondônia, Brazil.

The main cause of pulmonary tuberculosis (TB) is infection with Mycobacterium tuberculosis (MTB). We aimed to evaluate the contribution of nontuberculous mycobacteria (NTM) to pulmonary disease in patients from the state of Rondônia using respiratory samples and epidemiological data from TB cases. Mycobacterium isolates were identified using a combination of conventional tests, polymerase chain reaction-based restriction enzyme analysis of hsp65 gene and hsp65 gene sequencing. Among the 1,812 cases suspected of having pulmonary TB, 444 yielded bacterial cultures, including 369 cases positive for MTB and 75 cases positive for NTM. Within the latter group, 14 species were identified as Mycobacterium abscessus, Mycobacterium avium, Mycobacterium fortuitum, Mycobacterium intracellulare, Mycobacterium gilvum, Mycobacterium gordonae, Mycobacterium asiaticum, Mycobacterium tusciae, Mycobacterium porcinum, Mycobacterium novocastrense, Mycobacterium simiae, Mycobacterium szulgai, Mycobacterium phlei and Mycobacterium holsaticum and 13 isolates could not be identified at the species level. The majority of NTM cases were observed in Porto Velho and the relative frequency of NTM compared with MTB was highest in Ji-Paraná. In approximately half of the TB subjects with NTM, a second sample containing NTM was obtained, confirming this as the disease-causing agent. The most frequently observed NTM species were M. abscessus and M. avium and because the former species is resistant to many antibiotics and displays unsatisfactory cure rates, the implementation of rapid identification of mycobacterium species is of considerable importance.

Thulium laser vaporesection of prostates with volume exceeding 100 cm3 as an alternative to HoLEP and ThuLEP.

The aim of this study is to evaluate the outcomes of thulium laser vaporesection of prostates with volume exceeding 100 cm3. In the present prospective study, patients with infra-vesical urinary obstruction due to a prostate with volume exceeding 100 cm3 underwent endoscopic vaporesection using thulium laser. In this procedure, prostate chips were resected without morcellation. The technical aspects of surgery, admission time, post-operative catheter time and post-operative complications were analyzed. Flowmetry was performed combined with prostatic ultrasound in the follow-up. Between March 2010 and November 2018, 156 cases with benign prostatic hyperplasia (BPH; volume >100 cm3) were treated. The mean patient age was 67.8 years (48.4-86.6 years), and the mean prostatic volume was 137 cm3 (100-436 cm3). The mean length of hospitalization was 1.48 days (1-8 days), and the mean post-operative catheter time was 5.1 (1-17). Three cases (1.9%) required readmission due to hematuria. The mean follow-up time was 31.2 months (standard deviation = 27.7). Urethral stricture was observed in 14 cases (9%), with bulbar urethra being the most frequent finding. Urinary tract infection was observed in 11 cases (7.1%), and urinary incontinence was observed in 5 cases. The mean peak urinary flow at 12 and 24 months was 26.9 ± 12.5 and 23.9 ± 11.7 ml/s, respectively, and the mean urinary flow during the final follow-up at 41 months was 21.6 ml/s. Thulium laser vaporesection is a valid alternative to open prostatectomy, HoLEP and ThuLEP in patients with large BPH. Urinary flow remained elevated throughout the follow-up.

Patient Satisfaction with Healthcare Services and the Techniques Used for its Assessment: A Systematic Literature Review and a Bibliometric Analysis.

Patient satisfaction with healthcare provision services and the factors influencing it are be-coming the main focus of many scientific studies. Assuring the quality of the provided services is essential for the fulfillment of patients' expectations and needs. Thus, this systematic review seeks to find the determinants of patient satisfaction in a global setting. We perform an analysis to evaluate the collected literature and to fulfill the literature gap of bibliometric analysis within this theme. This review follows the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) approach. We conducted our database search in Scopus, Web of Science, and PubMed in June 2022. Studies from 2000-2021 that followed the inclusion and exclusion criteria and that were written in English were included in the sample. We ended up with 157 articles to review. A co-citation and bibliographic coupling analysis were employed to find the most relevant sources, authors, and documents. We divided the factors influencing patient satisfaction into criteria and explanatory variables. Medical care, communication with the patient, and patient's age are among the most critical factors for researchers. The bibliometric analysis revealed the countries, institutions, documents, authors, and sources most productive and significant in patient satisfaction.

First isolation of Mycobacterium kyorinense from clinical specimens in Brazil.

In this article, the first isolation of Mycobacterium kyorinense specimens in Brazil is described. M. kyorinense is a recently identified species, with a few strains reported only in Japan. The Brazilian isolates were initially identified as Mycobacterium celatum by PCR restriction enzyme pattern analysis (PRA) with hsp65. However, biochemical tests indicated the same profile of M. kyorinense and distinguished them from M. celatum and Mycobacterium branderi. The sequencing of the hsp65, rpoB, and 16S rRNA genes allowed the accurate identification of isolates as M. kyorinense.

Rapid tests for the detection of the Mycobacterium abscessus subsp. bolletii strain responsible for an epidemic of surgical-site infections in Brazil.

A single strain of Mycobacterium abscessus subsp. bolletii, characterised by a particular rpoB sequevar and two highly related pulsed field gel electrophoresis patterns has been responsible for a nationwide outbreak of surgical infections in Brazil since 2004. In this study, we developed molecular tests based on polymerase chain reaction restriction-enzyme analysis (PRA) and sequencing for the rapid identification of this strain. Sequences of 15 DNA regions conserved in mycobacteria were retrieved from GenBank or sequenced and analysed in silico. Single nucleotide polymorphisms specific to the epidemic strain and located in enzyme recognition sites were detected in rpoB, the 3' region of the 16S rDNA and gyrB. The three tests that were developed, i.e., PRA-rpoB, PRA-16S and gyrB sequence analysis, showed 100%, 100% and 92.31% sensitivity and 93.06%, 90.28% and 100% specificity, respectively, for the discrimination of the surgical strain from other M. abscessus subsp. bolletii isolates, including 116 isolates from 95 patients, one environmental isolate and two type strains. The results of the three tests were stable, as shown by results obtained for different isolates from the same patient. In conclusion, due to the clinical and epidemiological importance of this strain, these tests could be implemented in reference laboratories for the rapid preliminary diagnosis and epidemiological surveillance of this epidemic strain.

Fiber optic-based refractive index sensing at INESC Porto.

A review of refractive index measurement based on different types of optical fiber sensor configurations and techniques is presented. It addresses the main developments in the area, with particular focus on results obtained at INESC Porto, Portugal. The optical fiber sensing structures studied include those based on Bragg and long period gratings, on micro-interferometers, on plasmonic effects in fibers and on multimode interference in a large spectrum of standard and microstructured optical fibers.