WindowMasker: window-based masker for sequenced genomes

MOTIVATION: Matches to repetitive sequences are usually undesirable in the output of DNA database searches. Repetitive sequences need not be matched to a query, if they can be masked in the database. RepeatMasker/Maskeraid (RM), currently the most widely used software for DNA sequence masking, is slow and requires a library of repetitive template sequences, such as a manually curated RepBase library, that may not exist for newly sequenced genomes. RESULTS: We have developed a software tool called WindowMasker (WM) that identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself. WM is orders of magnitude faster than RM because WM uses a few linear-time scans of the genome sequence, rather than local alignment methods that compare each library sequence with each piece of the genome. We validate WM by comparing BLAST outputs from large sets of queries applied to two versions of the same genome, one masked by WM, and the other masked by RM. Even for genomes such as the human genome, where a good RepBase library is available, searching the database as masked with WM yields more matches that are apparently non-repetitive and fewer matches to repetitive sequences. We show that these results hold for transcribed regions as well. WM also performs well on genomes for which much of the sequence was in draft form at the time of the analysis. AVAILABILITY: WM is included in the NCBI C++ toolkit. The source code for the entire toolkit is available at ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/. Once the toolkit source is unpacked, the instructions for building WindowMasker application in the UNIX environment can be found in file src/app/winmasker/README.build. SUPPLEMENTARY INFORMATION: Supplementary data are available at ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/windowmasker/windowmasker_suppl.pdf     

The inclusion of the type III repeat ED-B in the fibronectin molecule generates conformational modifications that unmask a cryptic sequence.

We have previously reported an anti-fibronectin monoclonal antibody (mAb) (BC-1) which reacts with an ED-B-containing beta-galactosidase-fibronectin fusion protein but not with an identical beta-galactosidase-fibronectin fusion protein in which the ED-B sequence is omitted. In further experiments aimed at localizing more precisely the epitope recognized by this mAb, we demonstrate that 1) the mAb BC-1 is indeed specific for ED-B-containing fibronectin (FN) molecules even though the epitope recognized by this mAb is localized on the type III homology repeat 7 (the one which precedes the ED-B sequence) and 2) in fibronectin molecules lacking the ED-B sequence, this epitope is masked. We further demonstrate that, to mask the epitope recognized by the mAb BC-1, the presence of at least half of the FN type III homology repeat 9 is necessary. We also report the production of the mAb IST-6 which recognizes only FN molecules in which the ED-B sequence is lacking. These data clearly demonstrate that the presence of the ED-B sequence within FN molecules generates conformational modification in the central part of the molecules that unmasks previously cryptic sequences and masks others.     

The Effects of Face Masks on the Doctor-Patient Relationship in Orthopaedics

BackgroundSince the onset of the COVID-19 pandemic, the widespread use of face masks has grown exponentially. There is limited data highlighting the patient perception of face mask use during this pandemic, specifically in orthopaedic clinics. The purpose of this study was to determine the patient’s perception of the implementation of face masks in the orthopaedic clinic during a period of mask mandates and if this change impacted the success of their interactions with physicians. The secondary aim includes measures of patient satisfaction such as the ability to understand conversation and communicate effectively with the physician.MethodsParticipants were recruited on the day of their appointment at our institution’s orthopaedic clinic and provided with instructions via email. The online, anonymous survey included the CARE questionnaire - a tool to examine patient satisfaction by assessing perception of empathy and was conducted using Qualtrics.ResultsDoes patient preference to have their physician wear a face mask impact the success of their interactions with physicians? Overall, the use of face masks by physicians did not negatively impact patient encounters. CARE scores for patients who preferred masks (37.2) were similar to those who preferred their physician did not wear a mask (37.5). Is patient satisfaction affected by the use of face masks in the orthopaedic clinic? Patients who preferred that their doctor wear a face mask stated that it had no negative impact on the effect of communication or conversation with the physician. Other factors such as how well the patients knew the physician and patient gender had a greater impact on the CARE score than masks did.ConclusionOur study determined that the preference of face masks by patients does not impact the success of their interactions with physicians using the CARE score. The findings of this study are valuable in informing orthopaedic physicians about patient attitudes towards mask use and could influence decision making for not only the COVID-19 pandemic, but also future infectious outbreaks that may arise. Level of Evidence: III     

MC1R studies in dogs with melanistic mask or brindle patterns

Black mask is a characteristic pattern in which red, yellow, tan, fawn, or brindle dogs exhibit a melanistic muzzle which may extend up onto the ears. Melanistic mask is inherited in several breeds as an autosomal dominant trait, and appears to be a fixed trait in a few breeds of dogs. A MC1R nonsense mutation, R306ter, has been shown to cause a completely red or yellow coat color in certain breeds such as Irish setters, yellow Labrador retrievers, and golden retrievers. The amino acid sequence for the melanocortin receptor 1 gene (MC1R) was examined in 17 dogs with melanistic masks from seven breeds, 19 dogs without melanistic masks, and 7 dogs in which their coat color made the mask difficult to distinguish. We also examined nine brindle dogs of four breeds, including three dogs who also had a black mask. No consistent amino acid change was observed in the brindle dogs. All dogs with a melanistic mask had at least one copy of a valine substitution for methionine at amino acid 264 (M264V) and none were homozygous for the premature stop codon (R306ter). These results suggest that black mask, but not brindle, is caused by a specific MC1R allele.     

Development of motorized plasma lithography for cell patterning

The micropatterning of cells, which restricts the adhesive regions on the substrate and thus controls cell geometry, is used to study mechanobiology-related cell functions. Plasma lithography is a means of providing such patterns and uses a spatially-selective plasma treatment. Conventional plasma lithography employs a positionally-fixed mask with which the geometry of the patterns is determined and thus is not suited for producing on-demand geometries of patterns. To overcome this, we have manufactured a new device with a motorized mask mounted in a vacuum chamber of a plasma generator, which we designate motorized plasma lithography. Our pilot tests indicate that various pattern geometries can be obtained with the control of a shielding mask during plasma treatment. Our approach can thus omit the laborious process of preparing photolithographically microfabricated masks required for the conventional plasma lithography.     

Le dossier médical personnel du patient : réflexions sur le portail d’accès unique et le masquage du dossier

ObjectivesThe Social Security Finance Act of the 19th December 2007 specified two fundamental principles of the Personal Medical Record that raise a number of questions: the single portal and the masking of information.Materials and methodsAccording to the act, the existence of a portal will allow beneficiaries of National Health Insurance to manage both their Personal Medical Record and right of access of health-care professionals to the information therein and will ensure the control and traceability of access to Personal Medical Records. This is a major issue as much for the protection of patients’ privacy as for the promoters of the system and portal managers who could be held liable in cases of breaches of security. Moreover, the law provides for the right of the patient, or his/her legal representative to make certain information in the record inaccessible. Our thoughts bear on the methods that will be used to enable the health-care professional with access to the record to know or not to know what information contained in the record has been rendered inaccessible by the patient or his/her legal representative and what is meant by the term “masking of masks”. Masking of masks raises important questions because it could constitute a violation of the doctor patient relationship.ConclusionThough the patients’ right to mask the presence of masked information is not in question, the doctor should be informed, not about the nature of the masked information, but about its existence.     

Light-directed synthesis of peptide nucleic acids (PNAs) chips

We report herein the light-directed synthesis of peptide nucleic acids (PNAs) microarray using PNA monomers protected by photolabile protecting groups and a maskless technique that uses a digital micromirror array system to form virtual masks. An ultraviolet image from the virtual mask was cast onto the active surface of a glass substrate, which was mounted in a flow cell reaction chamber connected to a peptide synthesizer. Light exposure was followed by automatic chemical coupling cycles and these steps were repeated with different virtual masks to grow the desired PNA probes in a selected pattern. In a preliminary experiment, an array of PNA probes with dimensions of 4.11 mm × 4.11 mm was generated on each slide. Each synthesis region in the final array measured 210 μm × 210 μm for a total of 256 sites. The center-to-center space was 260 μm. It was observed from the hybridization pattern of the fluorescently labeled oligonucleotide targets that the fluorescence intensities of the matched, and mismatched sequences showed substantial difference, demonstrating specificity in the identification of complementary sequences. This opens the way to exploit processes from the microelectronics industry for the fabrication of PNA microarrays with high densities.     

Bugs with backpacks deter vision-guided predation by jumping spiders

As a case study of how insects use masks as a defence against vision-guided predators, an experimental study was carried out using Acanthaspis petax , a reduviid bug ('ant bug') that covers itself with a 'mask', or 'backpack', made from carcasses of its preferred prey (ants), and three salticid spider species, Hyllus sp., Plexippus sp. and Thyene sp., salticids being predators with exceptionally acute vision. The ant bugs and the salticids were from the Lake Victoria region of East Africa. In each test, a salticid was presented with a live bug or a lure made from a dead bug, with the mask removed ('naked') or intact ('masked'). Salticids made predatory responses to naked bugs significantly more often than to masked bugs. These findings suggest that salticids readily identify naked bugs as prey, but fail to identify masked bugs as prey.     

Integrating sequence with FPC fingerprint maps

Recent advances in both clone fingerprinting and draft sequencing technology have made it increasingly common for species to have a bacterial artificial clone (BAC) fingerprint map, BAC end sequences (BESs) and draft genomic sequence. The FPC (fingerprinted contigs) software package contains three modules that maximize the value of these resources. The BSS (blast some sequence) module provides a way to easily view the results of aligning draft sequence to the BESs, and integrates the results with the following two modules. The MTP (minimal tiling path) module uses sequence and fingerprints to determine a minimal tiling path of clones. The DSI (draft sequence integration) module aligns draft sequences to FPC contigs, displays them alongside the contigs and identifies potential discrepancies; the alignment can be based on either individual BES alignments to the draft, or on the locations of BESs that have been assembled into the draft. FPC also supports high-throughput fingerprint map generation as its time-intensive functions have been parallelized for Unix-based desktops or servers with multiple CPUs. Simulation results are provided for the MTP, DSI and parallelization. These features are in the FPC V9.3 software package, which is freely available.     

Searching for distantly related protein sequences in large databases by parallel processing on a transputer machine

AliMac is an implementation of a sensitive sequence alignmentalgorithm on a parallel computer. The method achieves reliablealignments for very distantly related sequences from a combineduse of amino acid exchange weights and physicochemical characteristics.The algorithm is computing intensive and its usage on conventionalcomputers is limited to a relatively small number of sequences.The parallel implementation uses a Macintosh Hex host computerand 21 transputers and achieves 22 times the speed of a VAX8650 at a fraction of the cost. This paper describes the AliMachardware and software and discusses problems and peculiaritiesof parallel implementations, especially with transputers. Finally,several popular sequence alignment algorithms are compared intheir ability to detect distantly related sequences in searchinglarge databases.     

安全、便捷技术再生一次性医用口罩的实验研究

在防控新型冠状病毒(2019 novel coronavirus, 2019-nCoV)疫情中,为了减少病毒的传播,一次性医用口罩是普通民众必不可缺少的防护品。然而,随着2019-nCoV的蔓延,口罩短缺现象严重。本研究旨在探讨一次性医用外科口罩(口罩)的再生方法,以达到既有个人防护的效果又能节省资源。用流行性感冒病毒(简称流感)模拟2019-nCoV污染口罩,采用常用的恒温烘箱干烤及电吹风机热风处理2种方法,对表面污染有流感病毒的医用口罩进行病毒灭活,洗脱口罩上已灭活处理的病毒,感染Mardin-Darby狗肾细胞(Mardin-Darby canine kidney cell,MDCK细胞),观察细胞病变并定量检测病毒基因组拷贝数以评价病毒灭活效果。同时采用抽滤系统和PM2.5监测仪对以2种相似热灭活方式处理过的口罩滤过截留PM2.5的效果进行评价。结果显示电吹风机30 min热风处理后病毒基因组拷贝数降低至原来的1/1 000 000～1/10 000 000,接近未感染组,但烘箱56 ℃ 30 min干热处理仅灭活部分病毒。2种热灭活方式对口罩的PM2.5滤过截留效果无显著影响。本研究提供了一个安全、便捷处理一次性医用外科口罩的方法,为个人防护用品口罩表面污染病毒的灭活及其再生利用提供了科学依据。然而,应注意的是在口罩匮乏的非常时期,普通人群可采用该简便技术再生口罩后再次使用,但该方法再生的口罩不适合密切接触患者的人群、医护人员及实验室工作人员使用。     

Can a combination of vaccination and face mask wearing contain the COVID-19 pandemic?

The COVID-19 pandemic is going into its third year with Europe again being the focus of major epidemic activity. The present review tries to answer the question whether one can come to grip with the pandemic by a combination of vaccinations and non-pharmaceutical interventions (NPIs). Several COVID-19 vaccines are of remarkable efficacy and achieve high protection rates against symptomatic disease, especially severe disease, but mathematical models suggest that the current vaccination coverage in many countries is insufficient to achieve pandemic control. NPIs are needed as complementary measures because recent research has also revealed the limits of vaccination alone. Here, we review the evidence for efficacy of face mask wearing in various settings. Overall pooled analysis showed significant reduction in COVID-19 incidence with mask wearing, although heterogeneity between studies was substantial. Controlled trials of mask wearing are difficult to conduct, separating mask wearing effects in population studies from the impact of other NPIs is challenging and the efficacy of masks depend on mask material and mask fit. The combination of vaccination and mask wearing is potentially synergistic since vaccination protects so far well from disease development (the omicron variant is currently an unknown) but immunity from infection wanes over few months after vaccination. In comparison, masks interfere with the virus transmission process at a level of a physical barrier independent of coronavirus variant. Vaccination and masks are much less costly to apply than other NPI measures which are associated with high economic and social costs, but paradoxically both measures are the target of a vocal opposition by a sizable minority of the society. In parallel with biomedical research, we need more social science research into this opposition to guide political decisions on how to end the pandemic.     

Determinants of skin contact pressure formation during non-invasive ventilation

There is no published data about mask features that impact skin contact pressure during mask ventilation.To investigate the physical factors of skin contact pressure formation.We measured masks with original and reduced air cushion size and recorded contact pressure. We determined cushion contact and mask areas by planimetric measurements.Contact pressures necessary to prevent air leakage during inspiration exceed inspiratory pressure by 1.01±0.41 hPa independent of cushion size.Contact area, ventilator pressure and mask area during inspiration and expiration impact contact pressure. Mask contact pressures are higher during expiration. The contact pressure increases with increase in inspiratory pressures independent of the ventilator cycle. During expiration, the contact pressure will increase in proportion to the expiratory pressure reduction of the ventilator. The mask with reduced air cushion size developed higher contact pressures.Contact pressure can be reduced by selecting masks with a small mask area in combination with a large mask cushion.     

Professional and home-made face masks reduce exposure to respiratory infections among the general population

Background

Governments are preparing for a potential influenza pandemic. Therefore they need data to assess the possible impact of interventions. Face-masks worn by the general population could be an accessible and affordable intervention, if effective when worn under routine circumstances.

Methodology

We assessed transmission reduction potential provided by personal respirators, surgical masks and home-made masks when worn during a variety of activities by healthy volunteers and a simulated patient.

Principal Findings

All types of masks reduced aerosol exposure, relatively stable over time, unaffected by duration of wear or type of activity, but with a high degree of individual variation. Personal respirators were more efficient than surgical masks, which were more efficient than home-made masks. Regardless of mask type, children were less well protected. Outward protection (mask wearing by a mechanical head) was less effective than inward protection (mask wearing by healthy volunteers).

Conclusions/Significance

Any type of general mask use is likely to decrease viral exposure and infection risk on a population level, in spite of imperfect fit and imperfect adherence, personal respirators providing most protection. Masks worn by patients may not offer as great a degree of protection against aerosol transmission.     

The role of iron in the formation of Ediacaran ‘death masks’

The Ediacara biota are an enigmatic group of Neoproterozoic soft-bodied fossils that mark the first major radiation of complex eukaryotic and macroscopic life. These fossils are thought to have been preserved via pyritic “death masks” mediated by seafloor microbial mats, though little about the chemical constraints of this preservational pathway is known, in particular surrounding the role of bioavailable iron in death mask formation and preservational fidelity. In this study, we perform decay experiments on both diploblastic and triploblastic animals under a range of simulated sedimentary iron concentrations, in order to characterize the role of iron in the preservation of Ediacaran organisms. After 28 days of decay, we demonstrate the first convincing “death masks” produced under experimental laboratory conditions composed of iron sulfide and probable oxide veneers. Moreover, our results demonstrate that the abundance of iron in experiments is not the sole control on death mask formation, but also tissue histology and the availability of nucleation sites. This illustrates that Ediacaran preservation via microbial death masks need not be a “perfect storm” of paleoenvironmental porewater and sediment chemistry, but instead can occur under a range of conditions.     

Some effects of repeated handling and the use of a mask on stress responses in zebu cattle during restraint

The objective of this investigation was to evaluate the effect of repeated handling and the use of a mask on the order of entry, temperament, cortisol concentration and heart and respiratory rates of Brahman cattle during restraint in a squeeze chute. In the first experiment, 18 cows were restrained in the chute for 10min on 19 test-days and blood samples were collected during five of the trials. Habituation to handling was reflected by a decrease in cortisol concentration as the study advanced (P<0.01). In the second experiment, conducted 6 months later, animals were randomly allotted to two groups, alternating the use of a mask over test-days while restraining the cows in the chute for 3min. Respiratory and heart rates were measured at the beginning and end of each 3min trial. A blood sample was also taken at the end of each trial. Respiratory rates decreased while the animals were restrained and this decrease tended to be greater (P=0.09) when the animals were wearing masks (3.06) than when not (2.2breaths/min). Heart rates also decreased and more so for masked animals (10.6beats/min) than for non-masked (5.0, P<0.01). Cortisol values tended to be higher (9.9 versus 4.7ng/ml, P=0.08) when animals were restrained without a mask. Temperament scores were lower (P>0.01) when cows were masked and have a relative high correlation (r=0.58) with flight distance values, (P<0.05). Finally, the order of entrance was found consistent over test-days, (P<0.01). It is concluded that Brahman cattle: (a) habituate to repeat handling in a squeeze chute; (b) are less emotionally reactive when their eyes were covered during this process and (c) establish a repeatable order of entrance to the chute.     

Repositioning accuracy of a novel thermoplastic mask for head and neck cancer radiotherapy

PurposeThe aim of this study was to assess the reproducibility of patient shoulder position immobilized with a novel and innovative prototype mask (E-Frame, Engineering System).MethodsThe E-frame mask fixes both shoulders and bisaxillary regions compared with that of a commercial mask (Type-S, CIVCO). Thirteen and twelve patients were immobilized with the Type-S and E-Frame mask systems, respectively. For each treatment fraction, cone-beam CT (CBCT) images of the patient were acquired and retrospectively analyzed. The CBCT images were registered to the planning CT based on the cervical spine, and then the displacements of the acromial extremity of the clavicle were measured.ResultsThe systematic and random errors between the two mask systems were evaluated. The differences of the systematic errors between the two mask systems were not statistically significant. The mean random errors in the three directions (AP, SI and LR) were 2.7 mm, 3.1 mm and 1.5 mm, respectively for the Type-S mask, and 2.8 mm 2.5 mm and 1.4 mm, respectively for the E-Frame mask. The random error of the E-Frame masks in the SI direction was significantly smaller than that of the Type-S. The number of cases showing displacements exceeding 10 mm in the SI direction for at least one fraction was eight (61% of 13 cases) and three (25% of 12 cases) for Type-S and E-Frame masks, respectively.ConclusionsThe E-Frame masks reduced the random displacements of patient’s shoulders in the SI direction, effectively preventing large shoulder shifts that occurred frequently with Type-S masks.     

Evaluation on masks with exhaust valves and with exhaust holes from physiological and subjective responses

The purpose of this study was to compare the effects of wearing different kinds of masks on the ear canal temperature, heart rate, clothing microclimate, and subjective perception of discomfort. Ten subjects performed intermittent exercise on a treadmill while wearing the protective masks in a climatic chamber controlled at an air temperature of 25 degrees C and a relative humidity of 70%. Two types of mask-mask A, with exhaust valves and mask B, with exhaust holes-were used in the study. The results of this study indicated: (1) The subjects had a tendency toward lower maximum heart rate when wearing mask A than when wearing mask B. (2) Temperatures and absolute humidities (the outer surface of mask, the microclimate inside the mask, the chest wall skin and microclimate) of mask A were significantly lower than those of mask B. (3) The ear canal temperature increased significantly in mask B as compared to that in mask A. (4) The ear canal temperature showed significant augmentation along with increased temperature and humidity inside the mask microclimate. The mask microclimate temperature also affected significantly the chest microclimate temperature. (5) Mask A was rated significantly lower for perception of humidity, heat, breath resistance, tightness, unfitness, odor, fatigue, and offered less overall discomfort than mask B. (6) Subjective preference for mask A was higher. (7) The ratings of subjective overall discomfort showed significant augmentation along with increased wetness and fatigue. We discuss how the ventilation properties of masks A and B induce significantly different temperature and humidity in the microclimates of the masks and the heat loss of the body, which have profound influences on heart rate, thermal stress, and subjective perception of discomfort.