Measurement of resonant bend loss in anti-resonant hollow core optical fiber: erratum.

An error on the part of the authors in drafting resulted in Eq. (3) being incorrect in the published paper [Opt. Express25, 20612 (2017)10.1364/OE.25.020612]. We present a corrected version of the equation. It should be noted that this does not affect the presented results or conclusions of the paper.

The hyoid as a sound conducting apparatus in laryngeally echolocating bats.

The morphology of the stylohyal-tympanic bone articulation found in laryngeally echolocating bats is highly indicative of a function associated with signal production. One untested hypothesis is that this morphology allows the transfer of a sound signal from the larynx to the tympanic bones (auditory bulla) via the hyoid apparatus during signal production by the larynx. We used µCT data and finite element analysis to model the propagation of sound through the hyoid chain into the tympanic bones to test this hypothesis. We modeled sound pressure (dB) wave propagation from the basihyal to the tympanic bones, vibratory behavior (m) of the stylohyal-tympanic bone unit, and the stylohyal and tympanic bones when the stylohyal bone is allowed to pivot on the tympanic bone. Sound pressure wave propagation was modeled using the harmonic acoustics solver in ANSYS and vibratory behavior was modeled using coupled modal and harmonic response analyses in ANSYS. For both analyses (harmonic acoustics and harmonic response), the input excitation on the basihyal and thyrohyals was modeled as the estimated pressure (Pa) imposed by the collision of the vibrating thyroid cartilage of the larynx against these bones during signal production. Our models support the hypothesis that this stereotypical hyoid morphology found in laryngeally echolocating bats can transfer sound to the auditory bullae at an amplitude that is likely heard for the species Artibeus jamaicensis and Rhinolophus pusillus.

Picosecond laser microwelding of AlSi-YAG for laser system assembly.

We report the successful picosecond laser welding of AlSi and YAG. This material combination is of significant interest to the field of laser design and construction. Parameter maps are presented that demonstrate the impact of pulse energy and focal position on the resultant weld. Weld performance relevant to industrial applications is measured, i.e., shear strength, process yield, and absolute thermal resistance are presented.

Reinforcement of the larynx and trachea in echolocating and non-echolocating bats.

The synchronization of flight mechanics with respiration and echolocation call emission by bats, while economizing these behaviors, presumably puts compressive loads on the cartilaginous rings that hold open the respiratory tract. Previous work has shown that during postnatal development of Artibeus jamaicensis (Phyllostomidae), the onset of adult echolocation call emission rate coincides with calcification of the larynx, and the development of flight coincides with tracheal ring calcification. In the present study, I assessed the level of reinforcement of the respiratory system in 13 bat species representing six families that use stereotypical modes of echolocation (i.e. duty cycle % and intensity). Using computed tomography, the degree of mineralization or ossification of the tracheal rings, cricoid, thyroid and arytenoid cartilages were determined for non-echolocators, tongue clicking, low-duty cycle low-intensity, low-duty cycle high-intensity, and high-duty cycle high-intensity echolocating bats. While all bats had evidence of cervical tracheal ring mineralization, about half the species had evidence of thoracic tracheal ring calcification. Larger bats (Phyllostomus hastatus and Pterpodidae sp.) exhibited more extensive tracheal ring mineralization, suggesting an underlying cause independent of laryngeal echolocation. Within most of the laryngeally echolocating species, the degree of mineralization or ossification of the larynx was dependent on the mode of echolocation system used. Low-duty cycle low-intensity bats had extensively mineralized cricoids, and zero to very minor mineralization of the thyroids and arytenoids. Low-duty cycle high-intensity bats had extensively mineralized cricoids, and patches of thyroid and arytenoid mineralization. The high-duty cycle high-intensity rhinolophids and hipposiderid had extensively ossified cricoids, large patches of ossification on the thyroids, and heavily ossified arytenoids. The high-duty cycle high-intensity echolocator, Pteronotus parnellii, had mineralization patterns and laryngeal morphology very similar to the other low-duty cycle high-intensity mormoopid species, perhaps suggesting relatively recent evolution of high-duty cycle echolocation in P. parnellii compared with the Old World high-duty cycle echolocators (Rhinolophidae and Hipposideridae). All laryngeal echolocators exhibited mineralized or ossified lateral expansions of the cricoid for articulation with the inferior horn of the thyroid, these were most prominent in the high-duty cycle high-intensity rhinolophids and hipposiderid, and least prominent in the low-duty cycle low-intensity echolocators. The non-laryngeal echolocators had extensively ossified cricoid and thyroid cartilages, and no evidence of mineralization/ossification of the arytenoids or lateral expansions of the cricoid. While the non-echolocators had extensive ossification of the larynx, it was inconsistent with that seen in the laryngeal echolocators.

The role of improved housing and living environments in malaria control and elimination.

Malaria risk and endemicity is often associated with the nature of human habitation and living environment. The disappearance of malaria from regions where it had been endemic for centuries, such as coastal areas of southern England, has been attributed, at least in part, to improvement in the quality of housing. Moreover, indigenous malaria transmission ceased throughout England without the necessity to eliminate the vector mosquitoes. The principles of malaria transmission, as formulated following the thinking of the pioneers of malaria epidemiology, Ronald Ross and George Macdonald, show how this may happen. Malaria ceases to be sustainable where its reproduction number, R0, the number of new cases generated on average for each existing case of malaria, falls below 1. In the terms of a Ross/Macdonald analysis the reduced contact between humans and blood-feeding mosquitoes that is achieved through housing that is secure against mosquito entry can have a powerful effect in reducing malaria R0. The island of Sri Lanka, where malaria had been endemic probably for centuries previously, has reported no indigenous cases of malaria since 2012. The disappearance of malaria from Sri Lanka followed an effective attack upon malaria transmission by the Sri Lanka Anti Malaria Campaign. The targeted and enhanced efforts of this campaign launched in 1999, drove the malaria R0 below 1 for most of the period up to 2012, leading to a nearly continuous decline in malaria cases until their extinction. The decades leading up to the launch of these efforts were ones of general improvement of living environment and notably in the quality of housing stock. Studies in the late 1980s had shown that quality of housing in a highly malarious district of Sri Lanka was a strong determinant of malaria risk. Through its effects on malaria R0, improved housing is likely to have facilitated the malaria control and cessation of indigenous malaria transmission in Sri Lanka and that it will help reduce the risk of the re-introduction of malaria to the island.

Impact of nonlinear effects on transmission losses of hollow-core antiresonant negative curvature optical fiber.

We investigate the impact of input pulse duration and peak power of a femtosecond laser on pulse broadening and propagation losses in selected hollow-core antiresonant fiber (HC-ARF). The mixed effects of strong self-phase modulation and relatively weak Raman scattering broaden the spectral width, which in turn causes a portion of the output spectrum to exceed the transmission band of the fiber, resulting in transmission losses. By designing and setting up a gas flow control system and a vacuum system, the nonlinear behavior of the fiber filled with different pressurized gases is investigated. The experimental results show that replacing the air molecules in the fiber core with argon can weaken pulse broadening and increase the transmittable peak power by 14 MW for a given 122 MW input, while a vacuum system can reduce the nonlinearity to a larger extent, therefore enhancing the transmission of HC-ARF by at least 26 MW.

The value of monitoring data in a process evaluation of hygiene behaviour change in Community Health Clubs to explain findings from a cluster-randomised controlled trial in Rwanda.

BACKGROUND: A cluster-Randomised Controlled Trial evaluation of the impact of the Community Health Clubs (CHCs) in the Community Based Environmental Health Promotion Programme in Rwanda in 2015 appeared to find little uptake of 7 hygiene indicators 1 year after the end of the intervention, and low impact on prevention of diarrhoea and stunting. METHODS: Monitoring data was revisited through detailed community records with all the expected inputs, outputs and external determinants analysed for fidelity to the research protocol. Five household inventory observations were taken over a 40-month period including 2 years after the end of the cRCT in a random selection of the 50 intervention CHCs and data compared to that of the trial. Focus Group Discussion with all Environmental Health Officers of the Ministry of Health provided context to understand the long-term community dynamics of hygiene behaviour change. RESULTS: It was found that the intervention had been jeopardised by external determinants with only 54% fidelity to protocol. By the end of the designated intervention period in June 2014, the treatment had reached only 58% of households with 41% average attendance at training sessions by the 4056 registered members and 51% mean completion rate of 20+ sessions. Therefore only 10% of 50 CHCs provided the full so-called 'Classic' training as per-protocol. However, sustainability of the CHCs was high, with all 50 being active 2 years after the end of the cRCT and over 80% uptake of recommended practices of the same 7 key indicators as the trial was achieved by 2017. CONCLUSIONS: The cRCT conclusion that the case study of Rusizi District does not encourage the use of the CHC model for scaling up, raises concerns over the possible misrepresentation of the potential of the holistic CHC model to achieve health impact in a more realistic time frame. It also questions the appropriateness of apparently rigorous quantitative research, such as the cluster-Randomised Controlled Trial as conducted in Rusizi District, to adequately assess community dynamics in complex interventions.

Rapid identification of genes controlling virulence and immunity in malaria parasites.

Identifying the genetic determinants of phenotypes that impact disease severity is of fundamental importance for the design of new interventions against malaria. Here we present a rapid genome-wide approach capable of identifying multiple genetic drivers of medically relevant phenotypes within malaria parasites via a single experiment at single gene or allele resolution. In a proof of principle study, we found that a previously undescribed single nucleotide polymorphism in the binding domain of the erythrocyte binding like protein (EBL) conferred a dramatic change in red blood cell invasion in mutant rodent malaria parasites Plasmodium yoelii. In the same experiment, we implicated merozoite surface protein 1 (MSP1) and other polymorphic proteins, as the major targets of strain-specific immunity. Using allelic replacement, we provide functional validation of the substitution in the EBL gene controlling the growth rate in the blood stages of the parasites.

TIM-3 Engagement Promotes Effector Memory T Cell Differentiation of Human Antigen-Specific CD8 T Cells by Activating mTORC1.

T cell expression of TIM-3 following Ag encounter has been associated with a continuum of functional states ranging from effector memory T cells to exhaustion. We have designed an in vitro culture system to specifically address the impact of anti-TIM-3/TIM-3 engagement on human Ag-specific CD8 T cells during a normal response to Ag and found that anti-TIM-3 treatment enhances T cell function. In our in vitro T cell culture system, MART1-specific CD8 T cells were expanded from healthy donors using artificial APCs. To ensure that the T cells were the only source of TIM-3, cells were rechallenged with peptide-loaded artificial APCs in the presence of anti-TIM-3 Ab. In these conditions, anti-TIM-3 treatment promotes generation of effector T cells as shown by acquisition of an activated phenotype, increased cytokine production, enhanced proliferation, and a transcription program associated with T cell differentiation. Activation of mTORC1 has been previously demonstrated to enhance CD8 T cell effector function and differentiation. Anti-TIM-3 drives CD8 T cell differentiation through activation of the mTORC1 as evidenced by increased levels of phosphorylated S6 protein and rhebl1 transcript. Altogether these findings suggest that anti-TIM-3, together with Ag, drives differentiation in favor of effector T cells via the activation of mTOR pathway. To our knowledge, this is the first report demonstrating that TIM-3 engagement during Ag stimulation directly influences T cell differentiation through mTORC1.

Using Hamiltonian Monte Carlo to estimate the log-linear cognitive diagnosis model via Stan.

The Bayesian literature has shown that the Hamiltonian Monte Carlo (HMC) algorithm is powerful and efficient for statistical model estimation, especially for complicated models. Stan, a software program built upon HMC, has been introduced as a means of psychometric modeling estimation. However, there are no systemic guidelines for implementing Stan with the log-linear cognitive diagnosis model (LCDM), which is the saturated version of many cognitive diagnostic model (CDM) variants. This article bridges the gap between Stan application and Bayesian LCDM estimation: Both the modeling procedures and Stan code are demonstrated in detail, such that this strategy can be extended to other CDMs straightforwardly.

Worldwide Engagement for Digitizing Biocollections (WeDigBio): The Biocollections Community's Citizen-Science Space on the Calendar.

The digitization of biocollections is a critical task with direct implications for the global community who use the data for research and education. Recent innovations to involve citizen scientists in digitization increase awareness of the value of biodiversity specimens; advance science, technology, engineering, and math literacy; and build sustainability for digitization. In support of these activities, we launched the first global citizen-science event focused on the digitization of biodiversity specimens: Worldwide Engagement for Digitizing Biocollections (WeDigBio). During the inaugural 2015 event, 21 sites hosted events where citizen scientists transcribed specimen labels via online platforms (DigiVol, Les Herbonautes, Notes from Nature, the Smithsonian Institution's Transcription Center, and Symbiota). Many citizen scientists also contributed off-site. In total, thousands of citizen scientists around the world completed over 50,000 transcription tasks. Here, we present the process of organizing an international citizen-science event, an analysis of the event's effectiveness, and future directions-content now foundational to the growing WeDigBio event.

The need for a standard approach to assessing the functionality of rural community water supplies.

The Sustainable Development Goals have set an agenda for transformational change in water access, aiming for secure household connections globally. Despite this goal, communal groundwater supplies are likely to remain the main source of improved water supplies for many rural areas in Africa and South Asia for decades to come. Understanding the poor functionality of existing communal supplies remains, therefore, a priority. A critical first step is to establish a sector-wide definition of borehole supply functionality and a standard method of its assessment.

Les objectifs du développement durable ont mis en place un programme de changement transformationnel de l'accès à l'eau, visant à assurer des connexions sûres des ménages à l'échelle mondiale. Malgré cet objectif, les approvisionnements en eaux souterraines à l'échelle communale sont susceptibles de demeurer le sujet principal à améliorer pour de nombreuses régions rurales d'Afrique et d'Asie du Sud pour les décennies à venir. La compréhension de la piètre fonctionnalité des approvisionnements existants à l'échelle communale reste donc une priorité. Une première étape cruciale consiste à établir une définition sectorielle de la fonctionnalité de l'approvisionnement par forage et une méthode normalisée de son évaluation.

Los objetivos de desarrollo sostenible han establecido una agenda para un cambio transformacional en el acceso al agua, con la finalidad de establecer conexiones domiciliarias seguras a nivel mundial. A pesar de este objetivo, es probable que los suministros comunales de agua subterránea sigan siendo la principal fuente de mejoras en el abastecimiento de agua para muchas áreas rurales en África y el sur de Asia en las próximas décadas. Entender la funcionalidad deficiente de los suministros comunales existentes sigue siendo, por lo tanto, una prioridad. Un primer paso crítico es establecer una definición sectorial de la funcionalidad del suministro de los pozos y un método estándar para su evaluación.

Os Objetivos de Desenvolvimento Sustentável estabeleceram uma agenda para mudanças de paradigmas no acesso à água, visando abastecimento doméstico em escala global. Apesar desse objetivo, os suprimentos comunitários de águas subterrâneas provavelmente continuarão a ser a principal fonte de abastecimento de água potável para muitas áreas rurais da África e do sul da Ásia por décadas. Compreender a baixa funcionalidade desses atuais suprimentos comunitários torna-se, portanto, prioritária. Um primeiro passo crítico é estabelecer uma definição setorial de funcionalidade de fornecimento de poços e um método padrão de avaliação.

Calcification of the lower respiratory tract in relation to flight development in Jamaican fruit bats (Phyllostomidae, Artibeus jamaicensis).

The production of echolocation calls in bats along with forces produced by contraction of thoracic musculature used in flight presumably puts relatively high mechanical loads on the lower respiratory tract (LRT). Thus, there are likely adaptations to prevent collapse or distortion of the bronchial tree and trachea during flight in echolocating bats. By clearing and staining (Alcian blue and Alizarin red) LRTs removed from nonvolant neonates, semivolant juveniles, volant subadults, and adult Jamaican fruit bats (Artibeus jamaicensis), I found that calcification of the tracheal, primary bronchial, and secondary bronchial (lobar) cartilage rings occurs over the span of about 3 days and coincides with later developmental stages of flight and the increased production of echolocation calls. Tracheal rings that are immediately adjacent to the larynx calcified first, followed by more caudal tracheal rings and then the rings of the primary and secondary bronchi. I suggest that calcification of LRT cartilage rings in echolocating bats provides increased rigidity to counter the thoracic compressions incurred during flight. Calcification of the LRT rings is an adaptation to support the emission of laryngeally produced echolocation calls during flight in bats.

Measurement of resonant bend loss in anti-resonant hollow core optical fiber.

We present the results of measurements of resonant spectral bend loss using a novel apparatus in a series of hollow core anti-resonant optical fibers, important for their applications in the delivery of industrial power ultra-short laser pulses. The measured bend losses exhibit clear wavelength-bend diameter resonances. We demonstrate, in good agreement with theoretical analysis, that the sensitivity to bend diameter (in terms of minimum bend radii) is dependent on the ratio between cladding and core structure size. By decreasing the cladding capillary diameter: core diameter ratio from 0.70 to 0.43 the minimum bend diameter is decreased from >160 mm to ~15 mm at a wavelength of 800 nm. Furthermore it is demonstrated that the exact position of the loss bands is highly dependent on the orientation of the fiber structure with the bend plane.

Towards industrial ultrafast laser microwelding: SiO2 and BK7 to aluminum alloy.

We report systematic analysis and comparison of ps-laser microwelding of industry relevant Al6082 parts to SiO2 and BK7. Parameter mapping of pulse energy and focal depth on the weld strength is presented. The welding process was found to be strongly dependent on the focal plane but has a large tolerance to variation in pulse energy. Accelerated lifetime tests by thermal cycling from -50° to +90°C are presented. Welds in Al6082-BK7 parts survive over the full temperature range where the ratio of thermal expansion coefficients is 3.4:1. Welds in Al6082-SiO2 parts (ratio 47.1:1) survive only a limited temperature range.

A comprehensive catalogue of somatic mutations from a human cancer genome.

All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights into the forces that have shaped this cancer genome. The dominant mutational signature reflects DNA damage due to ultraviolet light exposure, a known risk factor for malignant melanoma, whereas the uneven distribution of mutations across the genome, with a lower prevalence in gene footprints, indicates that DNA repair has been preferentially deployed towards transcribed regions. The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic.

DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families.

Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite's sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens.

As old as the mountains: the radiations of the Ericaceae.

Mountains are often more species-rich than lowlands. This could be the result of migration from lowlands to mountains, of a greater survival rate in mountains, or of a higher diversification rate in mountains. We investigated this question in the globally distributed family Ericaceae, which includes c. 4426 species ranging from sea level to > 5000 m. We predict that the interaction of low specific leaf area (SLA) and montane habitats is correlated with increased diversification rates. A molecular phylogeny of Ericaceae based on rbcL and matK sequence data was built and dated with 18 fossil calibrations and divergence time estimates. We identified radiations using bamm and correlates of diversification rate changes using binary-state speciation and extinction (BiSSE) and multiple-state speciation and extinction (MuSSE) analyses. Analyses revealed six largely montane radiations. Lineages in mountains diversified faster than nonmountain lineages (higher speciation rate, but no difference in extinction rate), and lineages with low SLA diversified faster than high-SLA lineages. Further, habitat and trait had a positive interactive effect on diversification. Our results suggest that the species richness in mountains is the result of increased speciation rather than reduced extinction or increased immigration. Increased speciation in Ericaceae was facilitated by low SLA.

Postnatal ontogeny of the cochlea and flight ability in Jamaican fruit bats (Phyllostomidae) with implications for the evolution of echolocation.

Recent evidence has shown that the developmental emergence of echolocation calls in young bats follow an independent developmental pathway from other vocalizations and that adult-like echolocation call structure significantly precedes flight ability. These data in combination with new insights into the echolocation ability of some shrews suggest that the evolution of echolocation in bats may involve inheritance of a primitive sonar system that was modified to its current state, rather than the ad hoc evolution of echolocation in the earliest bats. Because the cochlea is crucial in the sensation of echoes returning from sonar pulses, we tracked changes in cochlear morphology during development that included the basilar membrane (BM) and secondary spiral lamina (SSL) along the length of the cochlea in relation to stages of flight ability in young bats. Our data show that the morphological prerequisite for sonar sensitivity of the cochlea significantly precedes the onset of flight in young bats and, in fact, development of this prerequisite is complete before parturition. In addition, there were no discernible changes in cochlear morphology with stages of flight development, demonstrating temporal asymmetry between the development of morphology associated with echo-pulse return sensitivity and volancy. These data further corroborate and support the hypothesis that adaptations for sonar and echolocation evolved before flight in mammals.