Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of prognostic values of clinical and histopathologic characteristics in diffuse large B-cell lymphoma treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone therapy

The relationship between histopathologic characteristics and treatment outcomes in patients with diffuse large B-cell lymphoma (DLBCL) treated with rituximab-based immunochemotherapy needs re-evaluation. Patients with newly diagnosed DLBCL treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone (R-CHOP) were evaluated with respect to clinical characteristics, treatment efficacy, and survival. Immunohistochemistry of bcl-2, CD10, bcl-6, and MUM-1 was performed and patients were sub-classified as germinal center B-cell-like (GCB) or non-GCB type according to the Hans algorithm. There was no significant difference in overall survival (OS) between patients with GCB and those with non-GCB. Although there was no significant difference in OS between high-intermediate and high risk groups as classified by the standard International Prognostic Index (IPI; p = 0.50), all three groups with the revised IPI had a clear-cut separation for event-free survival and OS. The revised IPI better predicted survival than did the standard IPI in patients with DLBCL treated with R-CHOP. The Hans classification had no prognostic value.
Performance of turbo equalizers for optical PMD channels

This paper investigates the performance of iterative (turbo) equalization to mitigate the effects of a polarization-mode dispersion (PMD) in nonreturn-to-zero (NRZ) intensity-modulated optical-fiber transmission systems. A PMD can lead to severe distortions in the received electrical signal and is a key limiter for the development of high-bit-rate transmission over currently used fibers. In order to reduce the distortions due to a PMD, the performance of symbol-by-symbol maximum a posteriori (sbs-MAP) soft-in/soft-out (SISO) decoders is studied. The SISO algorithms are adapted to the noise statistics of the optical channel where the photo detector leads to a non-Gaussian signal-dependent noise at the receiver side. The modified SISO algorithms are successfully employed for turbo equalization and results show that iterative (turbo) equalization and decoding for the compensation of a PMD can lead to a tremendous reduction in the bit error ratio (BER). Moreover, it is shown that, due to the robustness of mutual information, the extrinsic information transfer (EXIT) chart can be applied for the design of iterative receivers in optical transmission systems even with a non-Gaussian noise
Differentiation of mouse embryonic stem cells in vitro: III. Morphological evaluation of tissues developed after implantation of differentiated mouse embryoid bodies

Mouse embryonic stem cells (ES) were allowed to differentiate in a liquid culture system. After 2–3 weeks, complex cystic embryoid bodies developed. These bodies were composed of several structures identified as cardiac muscle and yolk sac blood islands as well as cupshape compartments containing a mixed population of hematopoietic stem cells. When these cystic embryoid bodies were implanted into adult mice, either subcutaneously or under the kidney capsule, they developed into various tissues. These included bone, blood vessels, cardiac muscle, nerves, and skin with hair follicles. In addition, highly differentiated, complicated tissues resembling intestinal epithelium with mucus glands or salivary glandular tissue were derived. The ES tissues from these in vitro developed embryoid bodies developed quickly within 2 to 3 weeks of implantation. This is in contrast to a minimal of 6 weeks for teratocarcinomas derived from embryonic carcinoma cells and/or the direct implantation of undifferentiated embryonic stem cells. Moreover, we found that there are different types of tissue developed upon different sites of implantation. The data suggest a local environment and/or growth factors are influential for ES tissue development. This system provides a possible means to purify and identify stem cells that give rise to specific tissues, and to study the factors regulating the commitment of these stem cells. © 1993 Wiley‐Liss, Inc.
The effect of pulsation ratio on teat condition, milk somatic cell count and productivity in dairy cows in automatic milking

The pulsation ratio of a milking machine affects milk flow and milking time, and has also been reported to influence teat condition and milk somatic cell count (SCC). However, most studies comparing pulsation ratios have been performed on conventional cluster milking (whole-udder level), where effects such as deteriorated teat end condition and increased milk SCC are likely to be caused by over-milking on teats that are emptied faster than the other teats. When the teat cups are detached from each udder quarter separately which can be done in automatic milking systems (AMS), the risk of over-milking, especially in front teats, may be significantly reduced. This study investigated the effects of pulsation ratio on teat end condition, milk SCC, milk yield, milking time and milk flow in an automatic milking system where each udder quarter is milked separately. In total, 356 cows on five commercial farms were included in a split-udder design experiment comparing three pulsation ratios (60:40, 70:30 and 75:25) with the standard pulsation ratio (65:35) during 6 weeks. Pulsation rate was 60 cycles/min and vacuum level 46 kPa. The 70:30 and 75:25 ratios increased peak and average milk flow and the machine-on time was shorter with 75:25, while both peak and average milk flows were lower and machine-on time was longer with the 60:40 ratio. No negative effects on teat condition or milk SCC were observed with any of the pulsation ratios applied during the study. Thus it is possible that increased pulsation ratio can be used to increase milking efficiency in AMS where quarter milking is applied.
Particulate endocytosis mediates biological responses of human mesenchymal stem cells to titanium wear debris

Continual loading and articulation cycles undergone by metallic (e.g., titanium) alloy arthroplasty prostheses lead to liberation of a large number of metallic debris particulates, which have long been implicated as a primary cause of periprosthetic osteolysis and postarthroplasty aseptic implant loosening. Long‐term stability of total joint replacement prostheses relies on proper integration between implant biomaterial and osseous tissue, and factors that interfere with this integration are likely to cause osteolysis. Because multipotent mesenchymal stem cells (MSCs) located adjacent to the implant have an osteoprogenitor function and are critical contributors to osseous tissue integrity, when their functions or activities are compromised, osteolysis will most likely occur. To date, it is not certain or sufficiently confirmed whether MSCs endocytose titanium particles, and if so, whether particulate endocytosis has any effect on cellular responses to wear debris. This study seeks to clarify the phenomenon of titanium endocytosis by human MSCs (hMSCs), and investigates the influence of endocytosis on their activities. hMSCs incubated with commercially pure titanium particles exhibited internalized particles, as observed by scanning electron microscopy and confocal laser scanning microscopy, with time‐dependent reduction in the number of extracellular particles. Particulate endocytosis was associated with reduced rates of cellular proliferation and cell–substrate adhesion, suppressed osteogenic differentiation, and increased rate of apoptosis. These cellular effects of exposure to titanium particles were reduced when endocytosis was inhibited by treatment with cytochalasin D, and no significant effect was seen when hMSCs were treated only with conditioned medium obtained from particulate‐treated cells. These findings strongly suggest that the biological responses of hMSCs to wear debris are triggered primarily by the direct endocytosis of titanium particulates, and not mediated by secreted soluble factors. In this manner, therapeutical approaches that suppress particle endocytosis could reduce the bioreactivity of hMSCs to particulates, and enhance long‐term orthopedic implant prognosis by minimizing wear‐debris periprosthethic osteolysis. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 24:461–473, 2006
Molecular Pathways: Targeting Inhibitor of Apoptosis Proteins in Cancer—From Molecular Mechanism to Therapeutic Application

Inhibitor of apoptosis (IAP) proteins play a critical role in the control of survival and cell death by regulating key signaling events such as caspase activation and NF-κB signaling. Because aberrantly high expression of IAP proteins represents a frequent oncogenic event in human cancers, therapeutic targeting of IAP proteins is considered as a promising approach. Several small-molecule pharmacologic inhibitors of IAP proteins that mimic the binding domain of the endogenous IAP antagonist second mitochondrial activator of caspases (Smac) to IAP proteins have been developed over the past few years. IAP antagonists have been shown in various preclinical cancer models to either directly initiate cell death or, alternatively, to prime cancer cells for cytotoxic therapies by lowering the threshold for cell death induction. IAP antagonists (i.e., GDC-0917/CUDC-427, LCL161, AT-406, HGS1029, and TL32711) are currently under evaluation in early clinical trials alone or in combination regimens. Thus, the concept to therapeutically target IAP proteins in human cancer has in principle been successfully transferred into a clinical setting and warrants further evaluation as a treatment approach. Clin Cancer Res; 20(2); 289–95. ©2013 AACR.
Impact of double-balloon enteroscopy findings on the management of Crohn's disease

Abstract Objective. It is estimated that 10%–30% of Crohn's disease (CD) patients have small-bowel lesions, but the exact frequency and clinical relevance of these findings are unknown. Double-balloon enteroscopy (DBE) enables endoscopic visualization of the small bowel. The aim of this study was to evaluate the use of DBE for detecting small-bowel lesions in CD patients suspected of having small-bowel involvement. Furthermore, the clinical impact of adjusting treatment in these patients was assessed. Material and methods. A prospective study was performed in a tertiary referral center. CD patients suspected of small-bowel involvement and in whom distal activity had previously been excluded were included. All patients underwent DBE, followed by step-up therapy in patients with small-bowel lesions. The presence of small-bowel lesions during DBE was noted and clinical outcome was assessed after adjusting therapy. Results. Thirty-five patients (70%) showed small-bowel lesions; these lesions could not be assessed by conventional endoscopy in 23 (46%). At 1-year follow-up, step-up therapy in 26 patients (74%) led to clinical remission in 23 (88%). This was confirmed by a significant decrease in Crohn's disease activity index and mucosal repair on second DBE. Conclusions. DBE showed a high frequency of small-bowel lesions in known CD patients with clinically suspected small-bowel activity. Most of these lesions were not accessible for conventional endoscopy. Adjusting treatment in patients with small-bowel CD involvement led to clinical remission and mucosal repair in the majority of cases.
Design and Verification of a Pangenome Microarray Oligonucleotide Probe Set for Dehalococcoides spp

ABSTRACT Dehalococcoides spp. are an industrially relevant group of Chloroflexi bacteria capable of reductively dechlorinating contaminants in groundwater environments. Existing Dehalococcoides genomes revealed a high level of sequence identity within this group, including 98 to 100% 16S rRNA sequence identity between strains with diverse substrate specificities. Common molecular techniques for identification of microbial populations are often not applicable for distinguishing Dehalococcoides strains. Here we describe an oligonucleotide microarray probe set designed based on clustered Dehalococcoides genes from five different sources (strain DET195, CBDB1, BAV1, and VS genomes and the KB-1 metagenome). This “pangenome” probe set provides coverage of core Dehalococcoides genes as well as strain-specific genes while optimizing the potential for hybridization to closely related, previously unknown Dehalococcoides strains. The pangenome probe set was compared to probe sets designed independently for each of the five Dehalococcoides strains. The pangenome probe set demonstrated better predictability and higher detection of Dehalococcoides genes than strain-specific probe sets on nontarget strains with <99% average nucleotide identity. An in silico analysis of the expected probe hybridization against the recently released Dehalococcoides strain GT genome and additional KB-1 metagenome sequence data indicated that the pangenome probe set performs more robustly than the combined strain-specific probe sets in the detection of genes not included in the original design. The pangenome probe set represents a highly specific, universal tool for the detection and characterization of Dehalococcoides from contaminated sites. It has the potential to become a common platform for Dehalococcoides-focused research, allowing meaningful comparisons between microarray experiments regardless of the strain examined.
Adaptive subcarrier allocation and bit loading for voice/data transmission in multiuser OFDM systems

—This paper proposes a new algorithm of adaptive subcarrier allocation and bit loading for simultaneous voice and data transmission in multiuser OFDM systems. The algorithm dynamically assigns the number of subcarriers and bits/per symbol on each subcarrier for each user in a single cell. To cope with the stringent delay requirement of voice service, the subcarriers with low channel gains are assigned for voice transmission with a small number of bits per symbol to achieve the required bit error rate and transmission rate. With the remaining subcarriers, that generally have higher channel gains, and the transmission power, the throughput of data transmission is maximized by loading as many bits as possible on each subcarrier to achieve the required transmission rate and quality. Theoretical analysis and simulations on the proposed algorithm show that better performances are achieved compared to previously reported schemes.
Interventions for Stroke Rehabilitation: Analysis of the Research Contained in the OTseeker Evidence Database

Abstract Purpose: To analyse the stroke content in OTseeker in terms of the quantity of the research evidence, the quality of the randomised controlled trials (RCTs), and the types of interventions and outcome measures used. Method: A survey of stroke-related content in the OTseeker database was conducted in 2007. The year of publication and intervention categories used in each stroke-related RCT and systematic review (SR) were recorded. The internal validity of RCTs using the PEDro scale (partitioned) and the outcome measures used were also recorded. Results: Of the 4,369 articles indexed on OTseeker, 452 (10.3%) related to stroke were conducted between 1979 and 2006. The five most frequently studied intervention categories were movement training (43.2%), models of service delivery (31.2%), physical modalities/orthotics/splinting (30.1%), exercise/stretching/strength training (19.5%), and skill acquisition/training (9.3%). Random allocation (96.1%) was the most frequently satisfied internal validity criterion and therapist blinding (3.1%) was least often satisfied. The five most frequently used outcome measurement categories were basic and extended activities of daily living (70.1%), hand and upper limb function (56.1%), walking/gait (44.1%), movement/motor function (32.7%), and quality of life/general overall health (27.9%). Conclusion: The stroke-related content on OTseeker is useful for allied health professionals. This study highlights a need for better definitions of interventions and consensus about the best outcome measures. Few interventions or outcome measures were participation focused.
Enriched environment and physical activity stimulate hippocampal but not olfactory bulb neurogenesis

Exposure to an enriched environment and physical activity, such as voluntary running, increases neurogenesis of granule cells in the dentate gyrus of adult mice. These stimuli are also known to improve performance in hippocampus‐dependent learning tasks, but it is unclear whether their effects on neurogenesis are exclusive to the hippocampal formation. In this study, we housed adult mice under three conditions (enriched environment, voluntary wheel running and standard housing), and analysed proliferation in the lateral ventricle wall and granule cell neurogenesis in the olfactory bulb in comparison to the dentate gyrus. Using bromodeoxyuridine to label dividing cells, we could not detect any difference in the number of newly generated cells in the ventricle wall. When giving the new cells time to migrate and differentiate in the olfactory bulb, we observed no changes in the number of adult‐generated olfactory granule cells; however, voluntary running and enrichment produced a doubling in the amount of new hippocampal granule cells. The discrepancy between the olfactory bulb and the dentate gyrus suggests that these living conditions trigger locally through an as yet unidentified mechanism specific to neurogenic signals in the dentate gyrus.
Improved component carrier selection considering MPR information for LTE-A uplink systems

Carrier Aggregation (CA) is one of the key features introduced in LTE Release 10 to achieve higher levels of throughput. Two or more component carriers (CCs) are aggregated and user equipments (UEs) simultaneously transmit in more than one. The use of non-contiguous resource allocation in the uplink (UL) implies higher peak to average power ratio, so power de-rating is essential to avoid inter-modulation distortion and adjacent channel leakage-power ratio. CC selection is a key radio resource management procedure by which the eNB assigns UEs to CCs. While most CC selection algorithms deal with downlink, existing literature lacks efforts on UL CA. Moreover the mechanism is determinant on the UL performance. Given the UE power limitation, different criteria must be used in each link. This work proposes a novel CC selection algorithm that distinguishes between power limited and non-power limited UEs. In particular it is proposed to introduce information on maximum power reduction in selection decisions. Besides, UEs are not directly rejected if they are power limited, an acceptance margin is defined. This contains information on throughput variations between the allocation in several or just one CCs. This novel approach is contrasted with other CC selection techniques. Results show cell edge throughput improvements and the benefit of allowing bandwidth aggregation in a subset of power limited users.
Public Goods, Sustainable Development and Business Accountability: Connecting Corporate Performance and Preservation of the Commons

Sustainable Development is about preserving and maintaining public goods. This comes out both from the intraand intergenerational aspect of the Brundtland definition (“meeting the needs of the present without compromising the ability of future generations to meet their own needs”; World Commission on Environment and Development). In consequence, whoever uses public goods is liable for their preservation, for their maintenance and, where they are underdeveloped, for their built-up and expansion. “Paying” for the usage of public goods is taken care of by taxes and excise, and, more recently, by duties like those levied on emission. However, the magnitude of public goods usage is rarely measured on either national or regional or local levels (The phenomenon of global public goods is only briefly mentioned in the paper as it mainly studies the “macro-micro- linkage” between a national economy and business), let alone in monetary terms. Yet monetary valuation is the language of business, and when statistical indicators are set up to measure progress of sustainable development, there are almost none that link the macro-sphere to the business level. While the objective of national accounts is to serve for decision-making by government authorities in the first place, businesses and individuals do as well base their decisions on information gleaned from national accounts. Businesses are often reproached for using public goods for free. Therefore they might want to demonstrate that they earn a return on the capital invested in public goods they use; they might be interested to know the value of those goods, and they would wish to show that the taxes they pay are at least on par with the “return” on what is invested in public goods. The paper shows how this could be achieved, exhibiting the theoretical and practical issues and pointing to the obstacles that are blocking a fast solution.
Systematic Identification of Mycobacterium tuberculosis Effectors Reveals that BfrB Suppresses Innate Immunity*

Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter the human immune system. The effectors of Mtb play important roles in the interactions with the host. However, because of the lack of highly efficient strategies, there are only a handful of known Mtb effectors, thus hampering our understanding of Mtb pathogenesis. In this study, we probed Mtb proteome microarray with biotinylated whole-cell lysates of human macrophages, identifying 26 Mtb membrane proteins and secreted proteins that bind to macrophage proteins. Combining GST pull-down with mass spectroscopy then enabled the specific identification of all binders. We refer to this proteome microarray-based strategy as SOPHIE (Systematic unlOcking of Pathogen and Host Interacting Effectors). Detailed investigation of a novel effector identified here, the iron storage protein BfrB (Rv3841), revealed that BfrB inhibits NF-κB-dependent transcription through binding and reducing the nuclear abundance of the ribosomal protein S3 (RPS3), which is a functional subunit of NF- κB. The importance of this interaction was evidenced by the promotion of survival in macrophages of the mycobacteria, Mycobacterium smegmatis, by overexpression of BfrB. Thus, beyond demonstrating the power of SOPHIE in the discovery of novel effectors of human pathogens, we expect that the set of Mtb effectors identified in this work will greatly facilitate the understanding of the pathogenesis of Mtb, possibly leading to additional potential molecular targets in the battle against tuberculosis.