bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scalable microfluidics for single-cell RNA printing and sequencing
Authors: Bose Sayantan , Wan Zhenmao , Carr Ambrose , Rizvi Abbas H. , Vieira Gregory , Pe’er Dana , Sims Peter A. 
Published: June 2015

AbstractMany important biological questions demand single-cell transcriptomics on a large scale. Hence, new tools are urgently needed for efficient, inexpensive manipulation of RNA from individual cells. We report a simple platform for trapping single-cell lysates in sealed, picoliter microwells capable of printing RNA on glass or capturing RNA on beads. We then develop a scalable technology for genome-wide, single-cell RNA-Seq. Our device generates pooled libraries from hundreds of individual cells with consumable costs of $0.10–$0.20 per cell and includes five lanes for simultaneous experiments. We anticipate that this system will serve as a general platform for single-cell imaging and sequencing.
Impact of autoimmune risk alleles on the immune system
Authors: Ray John P , Hacohen Nir 
Published: June 2015

AbstractGenetic analyses of autoimmune diseases have revealed hundreds of disease-associated DNA variants, but the identity and function of the causal variants are understudied and warrant deeper mechanistic studies. Here, we highlight methods for deciphering how alleles that are associated with autoimmune disease alter the human immune system, and suggest strategies for future autoimmune genetic research.
Perceived barriers in the use of ultrasound in developing countries
Authors: Shah Sachita , Bellows Blaise A. , Adedipe Adeyinka A. , Totten Jodie E. , Backlund Brandon H. , Sajed Dana 
Published: June 2015

Abstract

Background
Access to ultrasound has increased significantly in resource-limited settings, including the developing world; however, there remains a lack of sonography education and ultrasound-trained physician support in developing countries. To further investigate this potential knowledge gap, our primary objective was to assess perceived barriers to ultrasound use in resource-limited settings by surveying care providers who practice in low- and middle-income settings.

Methods
A 25-question online survey was made available to health care providers who work with an ultrasound machine in low- and middle-income countries (LMICs), including doctors, nurses, technicians, and clinical officers. This was a convenience sample obtained from list-serves of ultrasound and radiologic societies. The survey was analyzed, and descriptive results were obtained.

Results
One hundred and thirty-eight respondents representing 44 LMICs including countries from the continents of Africa, South America, and Asia completed the survey, with a response rate of 9.6 %. Ninety-one percent of the respondents were doctors, and 9 % were nurses or other providers. Applications for ultrasound were diverse, including obstetrics (75 %), DVT evaluation (51 %), abscess evaluation (54 %), cardiac evaluation (64 %), inferior vena cava (IVC) assessment (49 %), Focused Assessment Sonography for Trauma (FAST) exam (64 %), biliary tree assessment (54 %), and other applications. The respondents identified the following barriers to use of ultrasound: lack of training (60 %), lack of equipment (45 %), ultrasound machine malfunction (37 %), and lack of ultrasound maintenance capability (47 %). Seventy-four percent of the respondents wished to have further training in ultrasound, and 82 % were open to receiving distance learning or telesonography training. Subjects used communication tools including Skype, Dropbox, emailed photos, and picture archiving and communication system (PACS) as ways to communicate and receive feedback on ultrasound images.

Conclusions
Health care providers in the developing world identify lack of training as a primary barrier to regular use of ultrasound in their practice. While equipment requirements including maintenance and cost of machines are also important factors, future research is warranted on best practices for training methods, including telesonography and distance learning to enhance ultrasound use in low-resource settings.
The role of beneficial bacteria wall elasticity in regulating innate immune response
Authors: Мokrozub Viktoria V. , Lazarenko Liudmyla M. , Sichel Liubov M. , Babenko Lidia P. , Lytvyn Petro M. , Demchenko Olga M. , Melnichenko Yulia O. , Boyko Nadiya V. , Biavati Bruno , DiGioia Diana , Bubnov Rostyslav V. , Spivak Mykola Ya 
Published: June 2015

Abstract

Background
Probiotics have great potential to contribute to development of healthy dietary regimes, preventive care, and an integrated approach to immunity-related disease management. The bacterial wall is a dynamic entity, depending on many components and playing an essential role in modulating immune response. The impact of cell wall elasticity on the beneficial effects of probiotic strains has not been sufficiently studied.
The aim was to investigate the effect of lactic acid bacteria (LAB) and bifidobacteria strains on phagocytic system cells (macrophages) as related to bacterial wall elasticity, estimated using atomic force microscopy (AFM).

Methods
We conducted studies on Balb/c line mice 18–20 g in weight using lyophilized strains of LAB—Lactobacillus acidophilus IMV B-7279, Lactobacillus casei IMV B-7280, Lactobacillus delbrueckii subsp. bulgaricus IMV B-7281, and bifidobacteria—Bifidobacterium animalis VKL and Bifidobacterium animalis VKB. We cultivated the macrophages obtained from the peritoneal cavity of mice individually with the strains of LAB and bifidobacteria and evaluated their effect on macrophages, oxygen-dependent bactericidal activity, nitric oxide production, and immunoregulatory cytokines. We used AFM scanning to estimate bacterial cell wall elasticity.

Results
All strains had a stimulating effect on the functional activity of macrophages and ability to produce NO/NO2 in vitro. Lactobacilli strains increased the production of IL-12 and IFN-γ in vitro. The AFM demonstrated different cell wall elasticity levels in various strains of LAB and bifidobacteria. The rigidity of the cell walls among lactobacilli was distributed as follows: Lactobacillus acidophilus IMV B-7279 > Lactobacillus casei IMV B-7280 > Lactobacillus delbrueckii subsp. bulgaricus IMV B-7281; among the strains of bifidobacteria: B. animalis VKB > B. animalis VKL. Probiotic strain survival in the macrophages depended on the bacterial cell wall elasticity and on the time of their joint cultivation.

Conclusion
LAB and bifidobacteria strains stimulate immune-modulatory cytokines and active oxygen and nitrogen oxide compound production in macrophages. Strains with a more elastic cell wall according to AFM data demonstrated higher resistance to intracellular digestion in macrophages and higher level of their activation.
AFM might be considered as a fast and accurate method to assess parameters of probiotic strain cell wall to predict their immune-modulatory properties.
The role and potential of umbilical cord blood in an era of new therapies: a review
Authors: Roura Santiago , Pujal Josep-Maria , Gálvez-Montón Carolina , Bayes-Genis Antoni 
Published: June 2015

AbstractIn light of pioneering findings in the 1980s and an estimation of more than 130 million global annual births, umbilical cord blood (UCB) is considered to be the most plentiful reservoir of cells and to have regenerative potential for many clinical applications. Although UCB is used mainly against blood disorders, the spectrum of diseases for which it provides effective therapy has been expanded to include non-hematopoietic conditions; UCB has also been used as source for regenerative cell therapy and immune modulation. Thus, collection and banking of UCB-derived cells have become a popular option. However, there are questions regarding the cost versus the benefits of UCB banking, and it also raises complex ethical and legal issues. This review discusses many issues surrounding the conservation of UCB-derived cells and the great potential and current clinical applications of UCB in an era of new therapies. In particular, we describe the practical issues inherent in UCB collection, processing, and long-term storage as well as the different types of ‘stem’ or progenitor cells circulating in UCB and their uses in multiple clinical settings. Given these considerations, the trend toward UCB will continue to provide growing assistance to health care worldwide.
A new application of cell-free bone regeneration: immobilizing stem cells from human exfoliated deciduous teeth-conditioned medium onto titanium implants using atmospheric pressure plasma treatment
Authors: Omori Masahiro , Tsuchiya Shuhei , Hara Kenji , Kuroda Kensuke , Hibi Hideharu , Okido Masazumi , Ueda Minoru 
Published: June 2015

Abstract
Introduction
Surface modification of titanium (Ti) implants promotes bone formation and shortens the osseointegration period. The aim of this study was to promote bone regeneration and stability around implants using atmospheric pressure plasma (APP) pretreatment. This was followed by immobilization of stem cells from human exfoliated deciduous teeth-conditioned medium (SHED-CM) on the Ti implant surface.

Methods
Ti samples (implants, discs, powder) were treated with APP for 30 seconds. Subsequently, these were immobilized on the treated Ti surface, soaked and agitated in phosphate-buffered saline or SHED-CM for 24 hours at 37 °C. The surface topography of the Ti implants was observed using scanning electron microscopy with energy dispersive X-ray spectroscopy. In vivo experiments using Ti implants placed on canine femur bone were then conducted to permit histological analysis at the bone-implant boundary. For the in vitro experiments, protein assays (SDS-PAGE, Bradford assay, liquid chromatography-ion trap mass spectrometry) and canine bone marrow stromal cell (cBMSC) attachment assays were performed using Ti discs or powder.

Results
In the in vitro study, treatment of Ti implant surfaces with SHED-CM led to calcium phosphate and extracellular matrix protein immobilization. APP pretreatment increased the amount of SHED-CM immobilized on Ti powder, and contributed to increased cBMSC attachment on Ti discs. In the in vivo study, histological analysis revealed that the Ti implants treated with APP and SHED-CM stimulated new bone formation around implants.

Conclusions
Implant device APP pretreatment followed by SHED-CM immobilization may be an effective application to facilitate bone regeneration around dental implants.
What quantitative mechanical loading stimulates in vitro cultivation best?
Authors: Natenstedt Jerry , Kok Aimee C , Dankelman Jenny , Tuijthof Gabrielle JM 
Published: June 2015

Abstract
Articular cartilage has limited regeneration capacities. One of the factors that appear to affect the in vitro cultivation of articular cartilage is mechanical stimulation. So far, no combination of parameters has been identified that offers the best results. The goal is to review the literature in search of the best available set of quantitative mechanical stimuli that lead to optimal in vitro cultivation.
The databases Scopus and PubMed were used to survey the literature, and strict in- and exclusion criteria were applied regarding the presence of quantitative data. The review was performed by studying the type of loading (hydrostatic compression or direct compression), the loading magnitude, the frequency and the loading regime (duration of the loading) in comparison to quantitative evidence of cartilage quality response (cellular, signaling and mechanical).
Thirty-three studies met all criteria of which 8 studied human, 20 bovine, 2 equine, 1 ovine, 1 porcine and 1 canine cells using four different types of cultivated constructs. Six studies investigated loading magnitude within the same setup, three studies the frequency, and seven the loading regime. Nine studies presented mechanical tissue response. The studies suggest that a certain threshold exits for enhanced cartilage in vitro cultivation of explants (>20 % strain and 0.5 Hz), and that chondrocyte-seeded cultivated constructs show best results when loaded with physiological mechanical stimuli. That is a loading pressure between 5–10 MPa and a loading frequency of 1 Hz exerted at intermittent intervals for a period of a week or longer. Critical aspects remain to be answered for translation into in vivo therapies.
Relative genomic stability of adipose tissue derived mesenchymal stem cells: analysis of ploidy, H19 long non-coding RNA and p53 activity
Authors: Ravid Orly , Shoshani Ofer , Sela Meirav , Weinstock Ada , Sadan Tommy Weiss , Gur Eyal , Zipori Dov , Shani Nir 
Published: June 2015

Abstract
Introduction
Mesenchymal stem cells (MSCs) are multipotent and have been derived from various tissues. Although MSCs share many basic features, they often display subtle tissue specific differences. We previously demonstrated that bone marrow (BM) MSCs frequently become polyploid in culture. This tendency was mediated by a reduction in the expression of H19 long non-coding RNA during the transition from a diploid to a polyploid state.

Methods
MSCs were derived from both BM and adipose tissue of mice and expanded under normoxic and hypoxic culture conditions. Cells were stained by propidium iodide and their ploidy was evaluated by FACS. Gene expression of independent MSC preparations was compared by quantitative real time PCR and protein expression levels by Western blot analysis. p53 silencing in MSCs was performed by a specific small hairpin RNA (shRNA).

Results
We set to examine whether genomic instability is common to MSCs originating from different tissues. It is demonstrated that adipose derived MSCs (ASCs) tend to remain diploid during culture while a vast majority of BM MSCs become polyploid. The diploid phenotype of ASCs is correlated with reduced H19 expression compared to BM MSCs. Under hypoxic conditions (3% oxygen) both ASCs and BM MSCs demonstrate increased RNA expression of H19 and Vascular endothelial growth factor A. Importantly, ASC gene expression is significantly less variable than BM MSCs under both oxygen conditions, indicating to their superior homogeneity. Gene expression analysis revealed that p53 target genes, often induced by DNA damage, are up-regulated in ASCs under basal conditions. However, p53 activation following treatment with DNA damaging agents was strongly elevated in BM MSCs compared to ASCs. We found that p53 is involved in maintaining the stable diploid state of ASCs as p53 shRNA induced ploidy changes in ASCs but not in BM MSCs.

Conclusions
The increased genomic stability of murine ASCs together with their lower H19 expression and relative homogeneity suggest a tissue specific higher stability of ASCs compared to BM MSCs, possibly due to higher activity of p53. The tissue specific differences between MSCs from a different tissue source may have important consequences on the use of various MSCs both in vitro and in vivo.
Human mesenchymal stem cells/multipotent stromal cells consume accumulated autophagosomes early in differentiation
Authors: Nuschke Austin , Rodrigues Melanie , Stolz Donna B , Chu Charleen T , Griffith Linda , Wells Alan 
Published: June 2015

Abstract
Introduction
Bone marrow mesenchymal stem cells/multipotent stromal cells (MSCs) are recruited to sites of injury and subsequently support regeneration through differentiation or paracrine activity. During periods of stress such as wound site implant or differentiation, MSCs are subjected to a variety of stressors that might activate pathways to improve cell survival and generate energy. In this study, we monitored MSC autophagy in response to the process of differentiation.

Methods
MSC autophagosome structures were observed by using transmission electron microscopy and a tandem green fluorescent protein-red fluorescent protein autophagic flux reporter to monitor the mammalian microtubule-associated protein-1 light chain 3 (LC3) turnover in real time. MSCs were differentiated by using standard osteogenic and adipogenic media, and autophagy was examined during short-term and long-term differentiation via immunoblots for LC3I and II. Autophagy was modulated during differentiation by using rapamycin and bafilomycin treatments to disrupt the autophagosome balance during the early stages of the differentiation process, and differentiation was monitored in the long term by using Von Kossa and Oil Red O staining as well as quantitative polymerase chain reaction analysis of typical differentiation markers.

Results
We found that undifferentiated MSCs showed an accumulation of a large number of undegraded autophagic vacuoles, with little autophagic turnover. Stimulation of autophagy with rapamycin led to rapid degradation of these autophagosomes and greatly increased rough endoplasmic reticulum size. Upon induction of osteogenic differentiation, MSC expression of LC3II, a common autophagosome marker, was lost within 12 hours, consistent with increased turnover. However, during adipogenic differentiation, drug treatment to alter the autophagosome balance during early differentiation led to changes in differentiation efficiency, with inhibited adipocyte formation following rapamycin treatment and accelerated fat accumulation following autophagosome blockade by bafilomycin.

Conclusions
Our findings suggest that MSCs exist in a state of arrested autophagy with high autophagosome accumulation and are poised to rapidly undergo autophagic degradation. This phenotype is highly sensitive, and a balance of autophagy appears to be key in efficient MSC differentiation and function, as evidenced by our results implicating autophagic flux in early osteogenesis and adipogenesis.
Human adipose-derived stromal/stem cells demonstrate short-lived persistence after implantation in both an immunocompetent and an immunocompromised murine model
Authors: Agrawal Hitesh , Shang Hulan , Sattah Anna Parker , Yang Ning , Peirce Shayn M , Katz Adam J 
Published: June 2015

Abstract
Introduction
Mesenchymal cells are emerging as a promising cell platform for regenerative therapies. However, the fate of cells after transplantation in many different disease settings and tissue beds remains unclear.

Methods
In this study, human adipose-derived stromal/stem (ASCs) cells were fluorescently labeled with a membrane dye and injected into both immunocompetent and immunocompromised mouse strains. Cells were injected either as single cell suspensions, or as self-assembling spheroids. In parallel, cells were purposefully devitalized prior to injection and then implanted in the opposite side in a randomized fashion. These ‘control’ groups were included to determine whether the fluorescent membrane dye would remain localized at the injection site despite the use of nonviable cells. Cell implants and the surrounding tissues were harvested on days 3, 10 and 21 after in vivo delivery and evaluated in a blinded manner. Injection sites were analyzed by fluorescent microscopy, and human cell numbers were quantified using PCR detection of a human-specific endogenous retrovirus (ERV-3). Host response was evaluated by immunofluorescent staining of macrophages.

Results
ERV-3 quantification showed that 95% of the human cells that were viable when they were injected were undetectable at the three-week time-point. Although fluorescent signal persisted for the entire study period, further analysis revealed that much of this signal was located within host macrophages.

Conclusions
These results suggest that human ASCs survive for less than three weeks after injection into even immunocompromised mice, and call into question the notion that human ASCs are immuno-privileged and capable of surviving for extended periods in xenogeneic and/or allogeneic models.
Adipose tissue derived stem cells: in vitro and in vivo analysis of a standard and three commercially available cell-assisted lipotransfer techniques
Authors: Domenis Rossana , Lazzaro Lara , Calabrese Sarah , Mangoni Damiano , Gallelli Annarita , Bourkoula Evgenia , Manini Ivana , Bergamin Natascha , Toffoletto Barbara , Beltrami Carlo A , Beltrami Antonio P , Cesselli Daniela , Parodi Pier Camillo 
Published: June 2015

Abstract
Introduction
Autologous fat grafting is commonly used to correct soft-tissue contour deformities. However, results are impaired by a variable and unpredictable resorption rate. Autologous adipose-derived stromal cells in combination with lipoinjection (cell-assisted lipotransfer) seem to favor a long-term persistence of fat grafts, thus fostering the development of devices to be used in the operating room at the point of care, to isolate the stromal vascular fraction (SVF) and produce SVF-enhanced fat grafts with safe and standardized protocols. Focusing on patients undergoing breast reconstruction by lipostructure, we analyzed a standard technique, a modification of the Coleman’s procedure, and three different commercially available devices (Lipokit, Cytori, Fastem), in terms of 1) ability to enrich fat grafts in stem cells and 2) clinical outcome at 6 and 12 months.

Methods
To evaluate the ability to enrich stem cells, we compared, for each patient (n = 20), the standard lipoaspirate with the respective stem cell-enriched one, analyzing yield, immunophenotype and colony-forming capacity of the SVF cells as well as immunophenotype, clonogenicity and multipotency of the obtained adipose stem cells (ASCs). Regarding the clinical outcome, we compared, by ultrasonography imaging, changes at 6 and 12 months in the subcutaneous thickness of patients treated with stem-cell enriched (n = 14) and standard lipoaspirates (n = 16).

Results
Both methods relying on the enzymatic isolation of primitive cells led to significant increase in the frequency, in the fat grafts, of SVF cells as well as of clonogenic and multipotent ASCs, while the enrichment was less prominent for the device based on the mechanical isolation of the SVF. From a clinical point of view, patients treated with SVF-enhanced fat grafts demonstrated, at six months, a significant superior gain of thickness of both the central and superior-medial quadrants with respect to patients treated with standard lipotransfer. In the median-median quadrant the effect was still persistent at 12 months, confirming an advantage of lipotransfer technique in enriching improving long-term fat grafts.

Conclusions
This comparative study, based on reproducible biological and clinical parameters and endpoints, showed an advantage of lipotransfer technique in enriching fat grafts in stem cells and in favoring, clinically, long-term fat grafts.