spacemaker

BACKGROUND: Spatial sequencing methods increasingly gain popularity within RNA biology studies. State-of-the-art techniques quantify messenger RNA expression levels from tissue sections and at the same time register information about the original locations of the molecules in the tissue. The resulting data sets are processed and analyzed by accompanying software that, however, is incompatible across inputs from different technologies. FINDINGS: Here, we present spacemake, a modular, robust, and scalable spatial transcriptomics pipeline built in Snakemake and Python...

This paper is in two parts. Part 1 examines the phenomenon of making space as a process involving one or other kind of legal decision-making, for example when a state authority authorizes the creation of a new highway along a certain route or of a new park in a certain location. In cases such as this, a new abstract spatial entity comes into existence - the route, the boundaries of the area to be set aside for the park - followed only later by concordant changes in physical reality. In Part 2, we show that features identified in studying this phenomenon of legal spacemaking can be detected in other spheres of human activity, for example in planning (where spacemaking is projected into the future), and in reasoning about history (where spacemaking is projected back through time)...

Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of inherited retinal degenerations. The ortholog of Drosophila eyes shut/spacemaker, EYS on chromosome 6q12 is a major genetic cause of recessive RP worldwide, with prevalence of 5 to 30%. In this study, by using targeted NGS, MLPA and Sanger sequencing we uncovered the EYS gene as one of the most common genetic cause of autosomal recessive RP in northern Sweden accounting for at least 16%. The most frequent pathogenic variant was c...

We describe a novel technique for the creation of a pleural tent and pleurectomy via the use of a laparoscopic hernia balloon. In this method a Spacemaker™ Structural Balloon Trocar (Covidien, USA) is tunnelled under the pleura at the site of thoracotomy or video assisted thoracoscopic surgery port and incrementally inflated under vision. This method is less traumatic than traditional methods, is more likely to provide an intact pleural tent, and allows the surgeon to operate in a near bloodless operative field...

BACKGROUND: Minimally invasive preperitoneal balloon tamponade (PPB) and abdominal aortic junctional tourniquets (AAJT) have been proposed as alternatives to open preperitoneal packing (OP) for the management of pelvic fracture-associated hemorrhage. We hypothesized that the PPB (SpaceMaker Pro) and AAJT would result in similar rates of survival and blood loss versus OP. METHODS: Thirty-two swine underwent creation of a combined open-book pelvic fracture and major iliac vascular injuries...

OBJECTIVE: Our aim was to evaluate a new inflatable lung retractor, the "Spacemaker", and its efficacy in facilitating minimally invasive cardiothoracic surgery without the need of one lung ventilation or carbon dioxide overpressure insufflation. METHODS: The device was tested in 12 anesthetized pigs (90-100 kg) placed on standard endotracheal ventilation. The device was introduced into the right or left side of the chest, depending on the intended procedure to be performed, via a 3-cm incision in the fifth intercostal space...

The unfolded protein response (UPR) is composed by homeostatic signaling pathways that are activated by excessive protein misfolding in the endoplasmic reticulum. Ire1 signaling is an important mediator of the UPR, leading to the activation of the transcription factor Xbp1. Here, we show that Drosophila Ire1 mutant photoreceptors have defects in the delivery of rhodopsin-1 to the rhabdomere and in the secretion of Spacemaker/Eyes Shut into the interrhabdomeral space. However, these defects are not observed in Xbp1 mutant photoreceptors...

Autogenous bone grafting remains a gold standard for the reconstruction critical-sized bone defects in the craniomaxillofacial region. Nevertheless, this graft procedure has several disadvantages such as restricted availability, donor-site morbidity, and limitations in regard to fully restoring the complicated three-dimensional structures in the craniomaxillofacial bone. The ultimate goal of craniomaxillofacial bone reconstruction is the regeneration of the physiological bone that simultaneously fulfills both morphological and functional restorations...

INTRODUCTION: Subfascial Endoscopic Perforator Surgery (SEPS) enables the direct visualization and section of perforating veins. Morbidity and duration of hospitalization are both less than with conventional open surgery (Linton's or Felder's techniques). PATIENTS AND METHODS: A total of 322 legs from 285 patients with a mean age of 56 years (range 23-90) were treated at our Department from May 1996 to January 2010. In 309 cases, an endoscope (ETM Endoskopische Technik GmbH, Berlin, Germany) was introduced through a transverse incision approximately 1...

BACKGROUND: Retinitis pigmentosa is the most important hereditary retinal degenerative disease, which has a high degree of clinical and genetic heterogeneity. More than half of all cases of retinitis pigmentosa are autosomal recessive (arRP), but the gene(s) causing arRP in most families has yet to be identified. The purpose of this study is to identify the genetic basis of severe arRP in a consanguineous Chinese family. METHODS: Linkage and haplotype analyses were used to define the chromosomal location of the pathogenic gene in the Chinese arRP family...

In patients with autosomal-recessive retinitis pigmentosa (arRP), homozygosity mapping was performed for detection of regions harboring genes that might be causative for RP. In one affected sib pair, a shared homozygous region of 5.0 Mb was identified on chromosome 6, within the RP25 locus. One of the genes residing in this interval was the retina-expressed gene EGFL11. Several genes resembling EGFL11 were predicted just centromeric of EGFL11. Extensive long-range RT-PCR, combined with 5'- and 3'- RACE analysis, resulted in the identification of a 10-kb transcript, starting with the annotated exons of EGFL11 and spanning 44 exons and 2 Mb of genomic DNA...

Using a positional cloning approach supported by comparative genomics, we have identified a previously unreported gene, EYS, at the RP25 locus on chromosome 6q12 commonly mutated in autosomal recessive retinitis pigmentosa. Spanning over 2 Mb, this is the largest eye-specific gene identified so far. EYS is independently disrupted in four other mammalian lineages, including that of rodents, but is well conserved from Drosophila to man and is likely to have a role in the modeling of retinal architecture.

This case series presents the use of acellular dermal matrix (ADM) as a barrier membrane in reconstructing non-spacemaking buccal dehiscences associated with simultaneous implant placement in locally deficient ridges. Five sites in four healthy nonsmoking patients were treated with a combination of the mucogingival pouch flap technique, sandwiched layering of mineralized human cancellous and cortical bone grafts, and ADM as a barrier membrane. Three sites encountered 2 to 4 mm of membrane exposure after 2 weeks of healing time...

The open rhabdoms of the fly's eye enhance absolute sensitivity but to avoid compromising spatial acuity they require precise optical geometry and neural connections.1 This neural superposition system evolved from the ancestral insect eye, which has fused rhabdoms. A recent paper by Zelhof and co-workers shows that the Drosophila gene spacemaker (spam) is necessary for development of open rhabdoms, and suggests that mutants revert to an ancestral state. Here I outline how open rhabdoms and neural superposition may have evolved via nocturnal intermediates, and discuss the implications for the role of spam in insect phylogeny...

Eyes differ markedly in the animal kingdom, and are an extreme example of the evolution of multiple anatomical solutions to light detection and image formation. A salient feature of all photoreceptor cells is the presence of a specialized compartment (disc outer segments in vertebrates, and microvillar rhabdomeres in insects), whose primary role is to accommodate the millions of light receptor molecules required for efficient photon collection. In insects, compound eyes can have very different inner architectures...

Most of the techniques that have been suggested for closure of sacral pressure sores use musculo-cutaneous flaps. We report our experience in three patients using the SpaceMaker balloon dissector. The dissector was inserted into the subgluteal maximus muscle plane to expand the muscle and overlying skin, thereby forming bilateral sliding and tension-free musculocutaneous flaps. The procedure is simple, safe, bloodless, and combines the advantages of advancement of a muscle flap and expansion.

The pectoralis major advancement flap is currently the most popular technique for reconstruction of the anterior chest in patients with sternotomy wounds. Recently, the SpaceMaker balloon was introduced for rapid expansion of the pectoralis major muscle intraoperatively. The aim of the present study was to investigate the biomechanical and histologic effects of this expansion technique in a rat model. The upper 2 cm of the sternum was resected in 54 male rats. Reconstruction with balloon-assisted pectoralis muscle expansion was performed in 24 rats (study group)...

Sternal wound infection is surgically treated by debridement of the infected sternum and closure of the defect with a muscular flap. These operations tend to be long, stressful, and time-consuming and to involve heavy blood loss. To facilitate wound closure, the SpaceMaker balloon was applied intraoperatively to expand the pectoralis major muscles and enable tensionless closure with musculocutaneous flaps. The aim of the present study was to compare the effectiveness and feasibility of this technique with a variety of others described in the literature...

Barrier membranes for guided tissue regeneration (GTR) to treat bone defects have to satisfy criteria of biocompatibility, cell-occlusiveness, spacemaking, tissue integration, and clinical manageability. In this study, the morphological and mechanical properties of two commercial biodegradable membranes (Resolut LT and Biofix) as a function of the incubation time have been compared. Moreover, their permeability to both fluids and epithelial cells as well as the bacteria adhesion have been evaluated. The membranes are asymmetric and composed of a dense polymeric layer coupled with nonwoven (Resolut LT) or woven (Biofix) fibers...

Applications of minimally invasive surgery have evolved from laparoscopic cholecystectomy and spread beyond conventional body cavities to new applications and disease processes. The purpose of the present study was to evaluate the feasibility of performing videoendoscopic thyroidectomy in a canine model. Adult mongrel dogs served as the experimental model for this study. The pretracheal space was entered via a 2.5-cm midline neck incision superior to the sternal notch and then expanded with a balloon spacemaker...