Passive Infrared Sensor-Based Occupancy Monitoring in Smart Buildings: A Review of Methodologies and Machine Learning Approaches.

Buildings are rapidly becoming more digitized, largely due to developments in the internet of things (IoT). This provides both opportunities and challenges. One of the central challenges in the process of digitizing buildings is the ability to monitor these buildings' status effectively. This monitoring is essential for services that rely on information about the presence and activities of individuals within different areas of these buildings. Occupancy information (including people counting, occupancy detection, location tracking, and activity detection) plays a vital role in the management of smart buildings. In this article, we primarily focus on the use of passive infrared (PIR) sensors for gathering occupancy information. PIR sensors are among the most widely used sensors for this purpose due to their consideration of privacy concerns, cost-effectiveness, and low processing complexity compared to other sensors. Despite numerous literature reviews in the field of occupancy information, there is currently no literature review dedicated to occupancy information derived specifically from PIR sensors. Therefore, this review analyzes articles that specifically explore the application of PIR sensors for obtaining occupancy information. It provides a comprehensive literature review of PIR sensor technology from 2015 to 2023, focusing on applications in people counting, activity detection, and localization (tracking and location). It consolidates findings from articles that have explored and enhanced the capabilities of PIR sensors in these interconnected domains. This review thoroughly examines the application of various techniques, machine learning algorithms, and configurations for PIR sensors in indoor building environments, emphasizing not only the data processing aspects but also their advantages, limitations, and efficacy in producing accurate occupancy information. These developments are crucial for improving building management systems in terms of energy efficiency, security, and user comfort, among other operational aspects. The article seeks to offer a thorough analysis of the present state and potential future advancements of PIR sensor technology in efficiently monitoring and understanding occupancy information by classifying and analyzing improvements in these domains.

Current clinical practice in the management of phyllodes tumors of the breast: an international cross-sectional study among surgeons and oncologists.

PURPOSE: Phyllodes tumors of the breast are rare fibroepithelial lesions that are classified as benign, borderline or malignant. There is little consensus on best practice for the work-up, management, and follow-up of patients with phyllodes tumors of the breast, and evidence-based guidelines are lacking. METHODS: We conducted a cross-sectional survey of surgeons and oncologists with the aim to describe current clinical practice in the management of phyllodes tumors. The survey was constructed in REDCap and distributed between July 2021 and February 2022 through international collaborators in sixteen countries across four continents. RESULTS: A total of 419 responses were collected and analyzed. The majority of respondents were experienced and worked in a university hospital. Most agreed to recommend a tumor-free excision margin for benign tumors, increasing margins for borderline and malignant tumors. The multidisciplinary team meeting plays a major role in the treatment plan and follow-up. The vast majority did not consider axillary surgery. There were mixed opinions on adjuvant treatment, with a trend towards more liberal regiments in patients with locally advanced tumors. Most respondents preferred a five-year follow-up period for all phyllodes tumor types. CONCLUSIONS: This study shows considerable variation in clinical practice managing phyllodes tumors. This suggests the potential for overtreatment of many patients and the need for education and further research targeting appropriate surgical margins, follow-up time and a multidisciplinary approach. There is a need to develop guidelines that recognize the heterogeneity of phyllodes tumors.

Angiosarcoma in the breast: a population-based cohort from Sweden.

BACKGROUND: Breast angiosarcoma is a rare disease mostly observed in breast cancer (BC) patients who have previously received radiotherapy (RT). Little is known about angiosarcoma aetiology, management, and outcome. The study aim was to estimate risk and to characterize breast angiosarcoma in a Swedish population-based cohort. METHODS: The Swedish Cancer Registry was searched for breast angiosarcoma between 1992 and 2018 in three Swedish healthcare regions (population 5.5 million). Information on previous BC, RT, management, and outcome were retrieved from medical records. RESULTS: Overall, 49 angiosarcomas located in the breast, chest wall, or axilla were identified, 8 primary and 41 secondary to BC treatment. Median age was 51 and 73 years, respectively. The minimum latency period of secondary angiosarcoma after a BC diagnosis was 4 years (range 4-21 years). The cumulative incidence of angiosarcoma after breast RT increased continuously, reaching 1.4‰ after 20 years. Among 44 women with angiosarcoma treated by surgery, 29 developed subsequent local recurrence. Median recurrence-free survival was 3.4 and 1.8 years for primary and secondary angiosarcoma, respectively. The 5-year overall survival probability for the whole cohort was 50 per cent (95 per cent c.i., 21 per cent-100 per cent) for primary breast angiosarcoma and 35 per cent (95 per cent c.i., 23 per cent-54 per cent) for secondary angiosarcoma. CONCLUSION: Breast angiosarcoma is a rare disease strongly associated with a history of previous BC RT. Overall survival is poor with high rates of local recurrences and distant metastasis.

Long-term outcome after surgical resection of non-high-risk gastrointestinal stromal tumours without adjuvant therapy.

BACKGROUND: Gastrointestinal stromal tumour (GIST) is the most common intra-abdominal sarcoma. Risk classification systems, commonly the modified National Institutes of Health consensus criteria, identify tumour properties relating to patient outcomes. However, owing to limited long-term evidence, most guidelines recommend up to 10-year follow-up for all risk groups except very low-risk GIST. METHODS: This retrospective multicentre study included patients who had complete resection of primary, non-metastatic GIST from three Scandinavian sarcoma centres: Gothenburg (2004-2020), Stockholm (2000-2019), and Oslo (2000-2017). Medical records were reviewed for clinical details regarding diagnosis, treatment, and follow-up, and recurrence-free and disease-specific survival evaluated. RESULTS: The total cohort consisted of 1213 patients with GIST. High-risk patients and those treated with tyrosine kinase inhibitors were excluded. The remaining 649 patients were included in the present analysis: 118 with very low-, 381 with low-, and 150 with intermediate-risk GISTs. Five-year recurrence-free survival rates were 100, 98.5, and 100 per cent for the intermediate-, low-, and very low-risk groups respectively (P = 0.246). Disease-specific survival rates 10 years after surgery were 100, 98.4, and 100 per cent for the intermediate-, low-, and very low-risk groups respectively (P = 0.262). CONCLUSION: Patients with completely resected non-high-risk GISTs have an excellent long-term outcome, irrespective of risk group. Follow-up programmes to detect disease recurrences in these patients are probably not indicated.

Gastrointestinal stromal tumours (GISTs) originate from the muscle layer of the gastrointestinal tract. They are divided into risk groups according to size, location, and how quickly they grow. Patients with GIST, regardless of risk group, have been followed with imaging for several years after their tumour has been successfully removed with an operation. The aim of this study was to evaluate whether follow-up is necessary for patients in the lower-risk groups. Six hundred and forty-nine patients with GISTs from the lower-risk groups were followed for 5 years (median). Only 1.2 per cent of the patients experienced a recurrence of their cancer. It was concluded that patients with GIST in the lower-risk groups do not need follow-up with imaging after a successful operation.

A Within-Subject Comparison of Face-to-Face and Telemedicine Screening Using the Timed Water Swallow Test (TWST) and the Test of Mastication and Swallowing of Solids (TOMASS).

The Timed Water Swallow Test (TWST) and the Test of Mastication of Solids (TOMASS) are dysphagia screening procedures that have been shown to be reliably assessed from video. The reliability of the procedures performed over telemedicine has not previously been assessed. TWST and TOMASS outcomes in two situations (both face-to-face and over telemedicine) were compared for 48 participants (aged 60-90; 27 with clinical conditions and 21 older persons). Both testing situation and test performed order were randomized, and all assessment procedures were performed within 3 h of each other. The results indicated a high level of agreement between face-to-face and telemedicine screening outcomes for TWST and TOMASS, respectively. The assessments indicated an 83% and 76% agreement in classifications of individual participants as within or outside normal limits for the TWST and TOMASS for the two test situations. The TWST showed a balanced distribution in differing classification in telemedicine (0.16-0.19 error rates). The TOMASS procedure classified more participants as outside normal limits over telemedicine compared to face-to-face administration. Agreement in the observed number of swallows was substantially lower than other outcome measures, which is attributed to increased difficulty in observing this property over video. Most participants (60%) reported that they would prefer telemedicine over face-to-face assessments, and 90% viewed the procedure as more accessible than expected. All participants were satisfied with the telemedicine procedures. The results suggest that clinical assessment of dysphagia over telemedicine using the TWST and TOMASS are viable alternatives to face-to-face administration of the procedures.

Testicular teratoma with nephroblastoma in an adult - case report and literature review.

Testicular germ cell tumours are the most common malignancies in young men. Germ cell tumours can be classified as seminomas or non-seminomas, each with different clinical features and treatment approaches. Germ cell tumours are occasionally associated with somatic-type malignancy, particularly in metastatic lymph nodes after adjuvant chemotherapy. Adenocarcinomas and rhabdomyosarcoma are the most common malignancies in this setting. In this report, we present a unique case of a 37-year-old patient who presented with a testicular teratoma containing a nephroblastoma component. The tumour exhibited characteristic morphology that resembled foetal kidney and expressed nuclear WT-1 and PAX-8 on immunohistochemistry. Following surgery, the patient opted for active surveillance and remains disease-free. To date, only 7 cases of nephroblastoma in primary testicular teratoma have been reported. This case highlights the importance of considering this rare entity in the differential diagnosis of testicular teratomas and the need for careful pathological examination.

The role of neoadjuvant imatinib in gastrointestinal stromal tumor patients: 20 years of experience from a tertial referral center.

Surgery is the cornerstone of gastrointestinal stromal tumor (GIST) treatment, and adjuvant therapy with imatinib has improved survival for high-risk tumors. The use of imatinib preoperatively has been increasing, but efficacy and impact on patient outcomes have not been formally investigated. This is a retrospective study from a single-center cohort of patients diagnosed with GIST and treated with neoadjuvant imatinib at Karolinska University Hospital in Stockholm, Sweden over a 20-year period. Eighty-four patients diagnosed with GIST and treated with neoadjuvant imatinib were identified and included. Tumors were located throughout the whole gastrointestinal tract but most frequently in the stomach (n = 29; 35%) and the small intestine (n = 30; 36%), followed by the rectum (n = 12; 14%) and the gastroesophageal junction (n = 10; 12%). The tumors were large (mean 10.5 cm) and decreased after treatment (mean 7.6 cm). Main indications for neoadjuvant imatinib were tumor size or anatomical location. None of the patients with stomach tumors and four patients with tumors near the gastroesophageal junction underwent gastrectomy. Three patients with tumors in the small intestine underwent pancreaticoduodenectomy, whereas seven patients with rectal tumors underwent rectal amputation. After surgery, 94% (n = 79) of the tumors had R0-resection. About one-fourth experienced local relapse or distant metastasis. In conclusion, neoadjuvant imatinib can reduce tumor size and prevent high morbidity due to more extensive surgery, or at least reduce the extent of the surgery, especially for tumors in the stomach or small intestine.

Dysregulation of COVID-19 related gene expression in the COPD lung.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) patients are at increased risk of poor outcome from Coronavirus disease (COVID-19). Early data suggest elevated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) receptor angiotensin converting enzyme 2 (ACE2) expression, but relationships to disease phenotype and downstream regulators of inflammation in the Renin-Angiotensin system (RAS) are unknown. We aimed to determine the relationship between RAS gene expression relevant to SARS-CoV-2 infection in the lung with disease characteristics in COPD, and the regulation of newly identified SARS-CoV-2 receptors and spike-cleaving proteases, important for SARS-CoV-2 infection. METHODS: We quantified gene expression using RNA sequencing of epithelial brushings and bronchial biopsies from 31 COPD and 37 control subjects. RESULTS: ACE2 gene expression (log2-fold change (FC)) was increased in COPD compared to ex-smoking (HV-ES) controls in epithelial brushings (0.25, p = 0.042) and bronchial biopsies (0.23, p = 0.050), and correlated with worse lung function (r = - 0.28, p = 0.0090). ACE2 was further increased in frequent exacerbators compared to infrequent exacerbators (0.51, p = 0.00045) and associated with use of ACE inhibitors (ACEi) (0.50, p = 0.0034), having cardiovascular disease (0.23, p = 0.048) or hypertension (0.34, p = 0.0089), and inhaled corticosteroid use in COPD subjects in bronchial biopsies (0.33, p = 0.049). Angiotensin II receptor type (AGTR)1 and 2 expression was decreased in COPD bronchial biopsies compared to HV-ES controls with log2FC of -0.26 (p = 0.033) and - 0.40, (p = 0.0010), respectively. However, the AGTR1:2 ratio was increased in COPD subjects compared with HV-ES controls, log2FC of 0.57 (p = 0.0051). Basigin, a newly identified potential SARS-CoV-2 receptor was also upregulated in both brushes, log2FC of 0.17 (p = 0.0040), and bronchial biopsies, (log2FC of 0.18 (p = 0.017), in COPD vs HV-ES. Transmembrane protease, serine (TMPRSS)2 was not differentially regulated between control and COPD. However, various other spike-cleaving proteases were, including TMPRSS4 and Cathepsin B, in both epithelial brushes (log2FC of 0.25 (p = 0.0012) and log2FC of 0.56 (p = 5.49E-06), respectively) and bronchial biopsies (log2FC of 0.49 (p = 0.00021) and log2FC of 0.246 (p = 0.028), respectively). CONCLUSION: This study identifies key differences in expression of genes related to susceptibility and aetiology of COVID-19 within the COPD lung. Further studies to understand the impact on clinical course of disease are now required.

Synthetic Generation of Passive Infrared Motion Sensor Data Using a Game Engine.

Quantifying the number of occupants in an indoor space is useful for a wide variety of applications. Attempts have been made at solving the task using passive infrared (PIR) motion sensor data together with supervised learning methods. Collecting a large labeled dataset containing both PIR motion sensor data and ground truth people count is however time-consuming, often requiring one hour of observation for each hour of data gathered. In this paper, a method is proposed for generating such data synthetically. A simulator is developed in the Unity game engine capable of producing synthetic PIR motion sensor data by detecting simulated occupants. The accuracy of the simulator is tested by replicating a real-world meeting room inside the simulator and conducting an experiment where a set of choreographed movements are performed in the simulated environment as well as the real room. In 34 out of 50 tested situations, the output from the simulated PIR sensors is comparable to the output from the real-world PIR sensors. The developed simulator is also used to study how a PIR sensor's output changes depending on where in a room a motion is carried out. Through this, the relationship between sensor output and spatial position of a motion is discovered to be highly non-linear, which highlights some of the difficulties associated with mapping PIR data to occupancy count.

Sarcoma of the breast: breast cancer history as etiologic and prognostic factor-A population-based case-control study.

PURPOSE: Sarcomas of the breast account for about 1% of all breast malignancies. The aim of this national survey was to explore etiologic and prognostic factors. METHODS: Utilizing national Swedish registers, all patients registered with mesenchymal tumors in the breast during the period 1993-2013 (n = 344) were identified and compared to up to ten age and gender matched controls. Cancer history was retrieved for cases and controls. Conditional Poisson regression models were used for calculation of odds ratios. RESULTS: Previous breast cancer was overrepresented among patients with angiosarcoma. The highest risk occurred ≥ 5 years after treatment for breast cancer (OR 73.9, 95% confidence interval, CI, 25.4-215; P < 0.001). An increase in incidence of angiosarcoma was observed during the study period (1.10, 95% CI 1.05-1.16; P < 0.001). The overall incidence of breast sarcoma increased from 1.52 to 2.04 cases per million per year. Angiosarcoma of the breast was associated with a significant excess mortality compared to age-matched controls (HR 4.65, 95% CI 3.01-7.19; P < 0.001). CONCLUSIONS: Angiosarcoma increased in incidence and displayed a more severe clinical course, with significantly shorter survival. The strong association between a history of breast cancer 5 years or more prior to the diagnosis of angiosarcoma points to radiotherapy as a contributing factor.

Single-cell study of neural stem cells derived from human iPSCs reveals distinct progenitor populations with neurogenic and gliogenic potential.

We used single-cell RNA sequencing (seq) on several human induced pluripotent stem (iPS) cell-derived neural stem cell (NSC) lines and one fetal brain-derived NSC line to study inherent cell type heterogeneity at proliferating neural stem cell stage and uncovered predisposed presence of neurogenic and gliogenic progenitors. We observed heterogeneity in neurogenic progenitors that differed between the iPS cell-derived NSC lines and the fetal-derived NSC line, and we also observed differences in spontaneous differentiation potential for inhibitory and excitatory neurons between the iPS cell-derived NSC lines and the fetal-derived NSC line. In addition, using a recently published glia patterning protocol we enriched for gliogenic progenitors and generated glial cells from an iPS cell-derived NSC line.

Decoding non-random mutational signatures at Cas9 targeted sites.

The mutation patterns at Cas9 targeted sites contain unique information regarding the nuclease activity and repair mechanisms in mammalian cells. However, analytical framework for extracting such information are lacking. Here, we present a novel computational platform called Rational InDel Meta-Analysis (RIMA) that enables an in-depth comprehensive analysis of Cas9-induced genetic alterations, especially InDels mutations. RIMA can be used to quantitate the contribution of classical microhomology-mediated end joining (c-MMEJ) pathway in the formation of mutations at Cas9 target sites. We used RIMA to compare mutational signatures at 15 independent Cas9 target sites in human A549 wildtype and A549-POLQ knockout cells to elucidate the role of DNA polymerase θ in c-MMEJ. Moreover, the single nucleotide insertions at the Cas9 target sites represent duplications of preceding nucleotides, suggesting that the flexibility of the Cas9 nuclease domains results in both blunt- and staggered-end cuts. Thymine at the fourth nucleotide before protospacer adjacent motif (PAM) results in a two-fold higher occurrence of single nucleotide InDels compared to guanine at the same position. This study provides a novel approach for the characterization of the Cas9 nucleases with improved accuracy in predicting genome editing outcomes and a potential strategy for homology-independent targeted genomic integration.

Assessment of speech impairment in patients with Parkinson's disease from acoustic quantifications of oral diadochokinetic sequences.

This investigation aimed at determining whether an acoustic quantification of the oral diadochokinetic (DDK) task may be used to predict the perceived level of speech impairment when speakers with Parkinson's disease (PD) are reading a standard passage. DDK sequences with repeated [pa], [ta], and [ka] syllables were collected from 108 recordings (68 unique speakers with PD), along with recordings of the speakers reading a standardized text. The passage readings were assessed in five dimensions individually by four speech-language pathologists in a blinded and randomized procedure. The 46 acoustic DDK measures were merged with the perceptual ratings of read speech in the same recording session. Ordinal regression models were trained repeatedly on 80% of ratings and acoustic DDK predictors per dimension in 10-folds, and evaluated in testing data. The models developed from [ka] sequences achieved the best performance overall in predicting the clinicians' ratings of passage readings. The developed [pa] and [ta] models showed a much lower performance across all dimensions. The addition of samples with severe impairments and further automation of the procedure is required for the models to be used for screening purposes by non-expert clinical staff.

Gut metagenome in European women with normal, impaired and diabetic glucose control.

Type 2 diabetes (T2D) is a result of complex gene-environment interactions, and several risk factors have been identified, including age, family history, diet, sedentary lifestyle and obesity. Statistical models that combine known risk factors for T2D can partly identify individuals at high risk of developing the disease. However, these studies have so far indicated that human genetics contributes little to the models, whereas socio-demographic and environmental factors have greater influence. Recent evidence suggests the importance of the gut microbiota as an environmental factor, and an altered gut microbiota has been linked to metabolic diseases including obesity, diabetes and cardiovascular disease. Here we use shotgun sequencing to characterize the faecal metagenome of 145 European women with normal, impaired or diabetic glucose control. We observe compositional and functional alterations in the metagenomes of women with T2D, and develop a mathematical model based on metagenomic profiles that identified T2D with high accuracy. We applied this model to women with impaired glucose tolerance, and show that it can identify women who have a diabetes-like metabolism. Furthermore, glucose control and medication were unlikely to have major confounding effects. We also applied our model to a recently described Chinese cohort and show that the discriminant metagenomic markers for T2D differ between the European and Chinese cohorts. Therefore, metagenomic predictive tools for T2D should be specific for the age and geographical location of the populations studied.

How Well Does Diadochokinetic Task Performance Predict Articulatory Imprecision? Differentiating Individuals with Parkinson's Disease from Control Subjects.

OBJECTIVE: To investigate whether syllables produced in an oral diadochokinetic (DDK) task may be quantified so that persons with Parkinson's disease (PD) perceived to have reduced articulatory precision when reading may be correctly identified using that quantification. PATIENTS AND METHODS: Syllable sequences from 38 speakers with PD and 38 gender- and age-matched control speakers (normal controls [NC]) were quantified acoustically and evaluated in terms of (1) the speakers' ability to accurately predict speaker group membership (PD or NC) and (2) their ability to predict reduced/non-reduced articulatory precision. RESULTS: A balanced accuracy of 80-93% in predicting speaker group membership was achieved. The best measures were related to the proportion of a syllable made up of a vowel, amplitude slope and syllable-to-syllable variation in duration and amplitude. The best material was that based on /ka/. Reduced articulatory precision was accurately predicted from DDK measures in 89% of the samples. Release-transient prominence and voicing during the onset of plosives were particularly strong predictors. CONCLUSIONS: DDK sequences can predict articulatory imprecision as observed in another speech task. The linking of performance across speech tasks probably requires measures of stability in syllable durations and amplitudes, as well as measures of subsyllabic acoustic features.

Wide Surgical Margin Improves the Outcome for Patients with Gastrointestinal Stromal Tumors (GISTs).

BACKGROUND: Surgical resection is still the main treatment for gastrointestinal stromal tumor (GIST), and R0 excision, regardless of surgical margins, is considered sufficient. METHODS: A cohort of 79 consecutive GIST cases treated at the Karolinska University Hospital, who were without metastasis at diagnosis and who had not received any pre-or postoperative treatment with tyrosine kinase inhibitors, was included. Surgical margins were evaluated at the time of surgery and classified as wide, marginal or intralesional. Time to local/peritoneal recurrence, distant metastasis, and survival were recorded. Cox regression analysis was used to investigate the association between surgical margin, and recurrence and survival. RESULTS: Local/peritoneal recurrence was diagnosed in 2/39 cases with wide margins, in 7/22 cases with marginal margins, and in 13/18 cases with intralesional surgery. Compared to wide margins this gives a hazard ratio of 6.8 (confidence interval 1.4-32.7) for marginal margins and 13.5 (3-61) for intralesional margins. In multivariate analysis, adjusting for size, site, and mitotic index, surgical margin remained an independent significant predictor of risk for recurrence. When classifying patients according to R0/R1 surgery, patients with R0 surgery showed longer time to peritoneal recurrence and better recurrence-free and disease-specific survival as compared to those with R1 resection. However, when excluding patients operated with wide surgical margin, no significant difference was observed. CONCLUSION: Wide surgical margins are of significant prognostic importance, supporting the strategy of en bloc resection with good margin and careful handling of the tumor to avoid damaging the peritoneal surface in surgical resection of GIST.

Unilateral Left Deep Brain Stimulation of the Caudal Zona Incerta Is Equally Effective on Voice Tremor as Bilateral Stimulation: Evidence from 7 Patients with Essential Tremor.

BACKGROUND/AIMS: Deep brain stimulation (DBS) is less effective on voice tremor than arm tremor, and it is generally assumed that successful voice tremor treatment requires bilateral DBS and possibly more precise thalamic stimulation. However, recent findings suggest that these assumptions should be reconsidered. OBJECTIVES: To evaluate whether unilateral DBS targeting the caudal zona incerta (cZi) may be sufficient to alleviate voice tremor in patients with essential tremor, or whether bilateral stimulation is needed. METHODS: Seven patients with voice tremor off stimulation were evaluated during bilateral stimulation using their clinical settings, and during unilateral left stimulation in iterations with increasing stimulation amplitude. Two expert listeners assessed voice tremor severity in all samples in a blinded procedure. RESULTS: Six patients had comparable or better effects with unilateral left stimulation compared to bilateral stimulation. For the seventh patient, unilateral DBS at a slightly higher amplitude achieved similar results as bilateral DBS. Overall, high-amplitude stimulation did not appear to be beneficial on voice tremor. CONCLUSIONS: Unilateral left and bilateral cZi-DBS had comparable effects on voice tremor in the investigated group of 7 patients. This finding suggests that the assumption that bilateral DBS is required to treat voice tremor may need to be reconsidered.

Metabolic effects of Lactobacillus reuteri DSM 17938 in people with type 2 diabetes: A randomized controlled trial.

AIMS: To investigate the metabolic effects of 12-week oral supplementation with Lactobacillus reuteri DSM 17938 in patients with type 2 diabetes on insulin therapy. MATERIALS AND METHODS: In a double-blind trial, we randomized 46 people with type 2 diabetes to placebo or a low (108 CFU/d) or high dose (1010 CFU/d) of L. reuteri DSM 17938 for 12 weeks. The primary endpoint was the effect of supplementation on glycated haemoglobin (HbA1c). Secondary endpoints were insulin sensitivity (assessed by glucose clamp), liver fat content, body composition, body fat distribution, faecal microbiota composition and serum bile acids. RESULTS: Supplementation with L. reuteri DSM 17938 for 12 weeks did not affect HbA1c, liver steatosis, adiposity or microbiota composition. Participants who received the highest dose of L. reuteri exhibited increases in insulin sensitivity index (ISI) and serum levels of the secondary bile acid deoxycholic acid (DCA) compared with baseline, but these differences were not significant in the between-group analyses. Post hoc analysis showed that participants who responded with increased ISI after L. reuteri supplementation had higher microbial diversity at baseline, and increased serum levels of DCA after supplementation. In addition, increases in DCA levels correlated with improvement in insulin sensitivity in the probiotic recipients. CONCLUSIONS: Intake of L. reuteri DSM 17938 for 12 weeks did not affect HbA1c in people with type 2 diabetes on insulin therapy; however, L. reuteri improved insulin sensitivity in a subset of participants and we propose that high diversity of the gut microbiota at baseline may be important.

Strategies to improve usability and preserve accuracy in biological sequence databases.

Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identification of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate postsubmission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data.

Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue.

Metagenomic sequencing has contributed important new knowledge about the microbes that live in a symbiotic relationship with humans. With modern sequencing technology it is possible to generate large numbers of sequencing reads from a metagenome but analysis of the data is challenging. Here we present the bioinformatics pipeline MEDUSA that facilitates analysis of metagenomic reads at the gene and taxonomic level. We also constructed a global human gut microbial gene catalogue by combining data from 4 studies spanning 3 continents. Using MEDUSA we mapped 782 gut metagenomes to the global gene catalogue and a catalogue of sequenced microbial species. Hereby we find that all studies share about half a million genes and that on average 300,000 genes are shared by half the studied subjects. The gene richness is higher in the European studies compared to Chinese and American and this is also reflected in the species richness. Even though it is possible to identify common species and a core set of genes, we find that there are large variations in abundance of species and genes.